def ensure_files(self, job, job_dir):
"""
Download remote files and find secondary files according to annotations
"""
inputs = job.app.inputs
self.input_collector = InputCollector(job_dir)
input_values = job.inputs
self._resolve(inputs, input_values, job.inputs)
def ensure_files(self, job, job_dir):
'''
Resolve paths of all input files
'''
inputs = job.app.inputs.io
self.input_collector = InputCollector(job_dir)
input_values = job.inputs
self._resolve(inputs, input_values, job.inputs)
class Container(object):
def __init__(self):
self.input_collector = None
def install(self, job):
pass
def get_mapping(self, paths):
return {}
def ensure_files(self, job, job_dir):
"""
Download remote files and find secondary files according to annotations
"""
inputs = job.app.inputs
self.input_collector = InputCollector(job_dir)
input_values = job.inputs
self._resolve(inputs, input_values, job.inputs)
def _resolve(self, inputs, input_values, job):
if inputs:
file_ins = [
i for i in inputs if isinstance(i.validator, NamedSchema)
and i.validator.name == 'File'
]
for f in file_ins:
val = input_values.get(f.id)
if val:
job[f.id] = map_or_apply(
lambda e: self.input_collector.download(
e.url,
f.input_binding.get('secondaryFiles')
if f.input_binding is not None else None), val)
class Container(object):
def __init__(self):
self.input_collector = None
def install(self, job):
pass
def get_mapping(self, paths):
return {}
def ensure_files(self, job, job_dir):
"""
Download remote files and find secondary files according to annotations
"""
inputs = job.app.inputs
self.input_collector = InputCollector(job_dir)
input_values = job.inputs
self._resolve(inputs, input_values, job.inputs)
def _resolve(self, inputs, input_values, job):
if inputs:
file_ins = [i for i in inputs
if isinstance(i.validator, NamedSchema) and
i.validator.name == 'File']
for f in file_ins:
val = input_values.get(f.id)
if val:
job[f.id] = map_or_apply(
lambda e: self.input_collector.download(
e.url, f.input_binding.get('secondaryFiles')
if f.input_binding is not None else None
),
val)
class Container(object):
def __init__(self):
self.input_collector = None
def install(self, job):
pass
def set_config(self, *args, **kwargs):
pass
def ensure_files(self, job, job_dir):
'''
Resolve paths of all input files
'''
inputs = job.app.inputs.io
self.input_collector = InputCollector(job_dir)
input_values = job.inputs
self._resolve(inputs, input_values, job.inputs)
def _resolve(self, inputs, input_values, job):
if inputs:
file_ins = [
i for i in inputs if isinstance(i.constructor, FileConstructor)
]
for f in file_ins:
val = input_values.get(f.id)
if val:
job[f.id] = map_or_apply(
lambda e: self.input_collector.download(
e.url,
f.annotations.get('secondaryFiles')
if f.annotations is not None else None), val)
def ensure_files(self, job, job_dir):
"""
Download remote files and find secondary files according to annotations
"""
inputs = job.app.inputs
self.input_collector = InputCollector(job_dir)
input_values = job.inputs
self._resolve(inputs, input_values, job.inputs)
