def __init__(self, job):
self.job = job
self.app = job.app
self._stdin = self.app.stdin
self._stdout = self.app.stdout
self.base_cmd = self.app.base_command
if isinstance(self.base_cmd, six.string_types):
self.base_cmd = self.base_cmd.split(' ')
self.args = self.app.arguments
self.eval = ExpressionEvaluator(job)
def __init__(self, job):
self.job = job
self.app = job.app
self._stdin = self.app.stdin
self._stdout = self.app.stdout
self.base_cmd = self.app.base_command
if isinstance(self.base_cmd, six.string_types):
self.base_cmd = self.base_cmd.split(' ')
self.args = self.app.arguments
self.eval = ExpressionEvaluator(job)
class CLIJob(object):
def __init__(self, job):
self.job = job
self.app = job.app
self._stdin = self.app.stdin
self._stdout = self.app.stdout
self.base_cmd = self.app.base_command
if isinstance(self.base_cmd, six.string_types):
self.base_cmd = self.base_cmd.split(' ')
self.args = self.app.arguments
self.eval = ExpressionEvaluator(job)
@property
def stdin(self):
if self._stdin:
return self.eval.resolve(self._stdin)
@property
def stdout(self):
if self._stdout:
return self.eval.resolve(self._stdout)
def make_arg_list(self):
adapters = [InputAdapter(a.get('valueFrom'), self.eval, {}, a)
for a in self.args]
ia = InputAdapter(self.job.inputs, self.eval, self.app.inputs)
args = ia.as_toplevel(adapters)
base_cmd = [self.eval.resolve(item) for item in self.base_cmd]
return [six.text_type(arg) for arg in base_cmd + args]
def cmd_line(self):
a = self.make_arg_list()
if self._stdin:
a += ['<', self.stdin]
if self._stdout:
a += ['>', self.eval.resolve(self.stdout)]
return ' '.join(a) # TODO: escape
def get_outputs(self, job_dir, job):
result, outs = {}, self.app.outputs
for out in outs:
out_binding = out.output_binding
ret = os.getcwd()
os.chdir(job_dir)
pattern = self.eval.resolve(out_binding.get('glob')) or ""
files = glob.glob(pattern)
result[out.id] = [
{
'path': os.path.abspath(p),
'size': os.stat(p).st_size,
# 'checksum': 'sha1$' +
# hashlib.sha1(open(os.path.abspath(p)).read()).hexdigest(),
'metadata': meta(p, job.inputs, self.eval, out_binding),
'secondaryFiles': secondary_files(p, out_binding, self.eval)
} for p in files]
os.chdir(ret)
if out.depth == 0:
result[out.id] = result[out.id][0] if result[out.id] else None
return result
def run(self, job):
self.load_input_content(job)
result = ExpressionEvaluator.evaluate(
self.engine, self.script, job.to_dict(self.context), None
)
return result
def run(self, job):
self.load_input_content(job)
result = ExpressionEvaluator.evaluate(self.engine, self.script,
job.to_dict(self.context), None)
return result
class CLIJob(object):
def __init__(self, job):
self.job = job
self.app = job.app
self._stdin = self.app.stdin
self._stdout = self.app.stdout
self.base_cmd = self.app.base_command
if isinstance(self.base_cmd, six.string_types):
self.base_cmd = self.base_cmd.split(' ')
self.args = self.app.arguments
self.eval = ExpressionEvaluator(job)
@property
def stdin(self):
if self._stdin:
return self.eval.resolve(self._stdin)
@property
def stdout(self):
if self._stdout:
return self.eval.resolve(self._stdout)
def make_arg_list(self):
adapters = [
InputAdapter(a.get('valueFrom'), self.eval, {}, a)
for a in self.args
]
ia = InputAdapter(self.job.inputs, self.eval, self.app.inputs)
args = ia.as_toplevel(adapters)
base_cmd = [self.eval.resolve(item) for item in self.base_cmd]
return [six.text_type(arg) for arg in base_cmd + args]
def cmd_line(self):
a = self.make_arg_list()
if self._stdin:
a += ['<', self.stdin]
if self._stdout:
a += ['>', self.eval.resolve(self.stdout)]
return ' '.join(a) # TODO: escape
def get_outputs(self, job_dir, job):
result, outs = {}, self.app.outputs
for out in outs:
out_binding = out.output_binding
ret = os.getcwd()
os.chdir(job_dir)
pattern = self.eval.resolve(out_binding.get('glob')) or ""
files = glob.glob(pattern)
result[out.id] = [
{
'path': os.path.abspath(p),
'size': os.stat(p).st_size,
# 'checksum': 'sha1$' +
# hashlib.sha1(open(os.path.abspath(p)).read()).hexdigest(),
'metadata': meta(p, job.inputs, self.eval, out_binding),
'secondaryFiles': secondary_files(p, out_binding,
self.eval)
} for p in files
]
os.chdir(ret)
if out.depth == 0:
result[out.id] = result[out.id][0] if result[out.id] else None
return result
