def load_file_content(self, binding, val):
load = binding and binding.get('loadContents')
if load:
map_rec_collection(
lambda x: x.load_content() if isinstance(x, File) else None,
val
)
def collect_files(inputs):
files = []
def append_file(v):
if isinstance(v, File):
files.append(v)
map_rec_collection(append_file, inputs)
return files
def collect_files(inputs):
files = []
def append_file(v):
if isinstance(v, File):
files.append(v)
map_rec_collection(append_file, inputs)
return files
def get_inputs(app, args, basedir=None):
basedir = basedir or os.path.abspath('.')
inputs = app.construct_inputs(args)
return map_rec_collection(
lambda v: rebase_path(v, basedir),
inputs
)
def run(self, job, job_dir=None):
job_dir = os.path.abspath(job_dir or job.id)
if not job_dir.endswith('/'):
job_dir += '/'
os.mkdir(job_dir)
os.chmod(job_dir,
os.stat(job_dir).st_mode | stat.S_IROTH | stat.S_IWOTH)
self.cli_job = CLIJob(job)
if self.container:
self.ensure_files(job, job_dir)
abspath_job = Job(job.id, job.app, copy.deepcopy(job.inputs),
job.allocated_resources, job.context)
self.install(job=job)
cmd_line = self.command_line(job, job_dir)
self.job_dump(job, job_dir)
self.container.run(cmd_line, job_dir)
result_path = os.path.abspath(job_dir) + '/result.cwl.json'
if os.path.exists(result_path):
with open(result_path, 'r') as res:
outputs = json.load(res)
else:
with open(result_path, 'w') as res:
outputs = self.cli_job.get_outputs(
os.path.abspath(job_dir), abspath_job)
json.dump(outputs, res)
outputs = {
o.id: construct_files(outputs.get(o.id), o.validator)
for o in job.app.outputs
}
self.unmap_paths(outputs)
def write_rbx(f):
if isinstance(f, File):
with open(f.path + '.rbx.json', 'w') as rbx:
json.dump(f.to_dict(), rbx)
map_rec_collection(write_rbx, outputs)
return outputs
def run(self, job, job_dir=None):
job_dir = os.path.abspath(job_dir or job.id)
if not job_dir.endswith('/'):
job_dir += '/'
os.mkdir(job_dir)
os.chmod(job_dir, os.stat(job_dir).st_mode | stat.S_IROTH |
stat.S_IWOTH)
self.cli_job = CLIJob(job)
if self.container:
self.ensure_files(job, job_dir)
abspath_job = Job(
job.id, job.app, copy.deepcopy(job.inputs),
job.allocated_resources, job.context
)
self.install(job=job)
cmd_line = self.command_line(job, job_dir)
self.job_dump(job, job_dir)
self.container.run(cmd_line, job_dir)
result_path = os.path.abspath(job_dir) + '/result.cwl.json'
if os.path.exists(result_path):
with open(result_path, 'r') as res:
outputs = json.load(res)
else:
with open(result_path, 'w') as res:
outputs = self.cli_job.get_outputs(
os.path.abspath(job_dir), abspath_job)
json.dump(outputs, res)
outputs = {o.id: construct_files(outputs.get(o.id), o.validator)
for o in job.app.outputs}
self.unmap_paths(outputs)
def write_rbx(f):
if isinstance(f, File):
with open(f.path + '.rbx.json', 'w') as rbx:
json.dump(f.to_dict(), rbx)
map_rec_collection(write_rbx, outputs)
return outputs
def get_inputs(args, inputs, basedir=None):
basedir = basedir or os.path.abspath('.')
constructed = {}
for i in inputs:
val = args.get(i.id)
if i.depth == 0:
cons = construct_files(val, i.validator)
else:
cons = [construct_files(e, i.validator)
for e in val] if val else []
if cons:
constructed[i.id] = cons
return map_rec_collection(lambda v: rebase_path(v, basedir), constructed)
def get_inputs(args, inputs, basedir=None):
basedir = basedir or os.path.abspath('.')
constructed = {}
for i in inputs:
val = args.get(i.id)
if i.depth == 0:
cons = construct_files(val, i.validator)
else:
cons = [construct_files(e, i.validator) for e in val] if val else []
if cons:
constructed[i.id] = cons
return map_rec_collection(
lambda v: rebase_path(v, basedir),
constructed
)
def load_file_content(self, binding, val):
load = binding and binding.get('loadContents')
if load:
map_rec_collection(
lambda x: x.load_content()
if isinstance(x, File) else None, val)
def run(self, job, job_dir=None):
self.load_input_content(job)
job_dir = os.path.abspath(job_dir or job.id)
if not job_dir.endswith('/'):
job_dir += '/'
if not os.path.exists(job_dir):
os.mkdir(job_dir)
os.chmod(job_dir, os.stat(job_dir).st_mode | stat.S_IROTH |
stat.S_IWOTH)
self.cli_job = CLIJob(job)
eval = ValueResolver(job)
cfr = self.get_requirement_or_hint(CreateFileRequirement)
if cfr:
cfr.create_files(job_dir, eval)
env = None
evr = self.get_requirement_or_hint(EnvVarRequirement)
if evr:
env = evr.var_map(eval)
self.ensure_files(job, job_dir)
self.install(job=job)
abspath_job = Job(
job.id, job.app, copy.deepcopy(job.inputs),
job.allocated_resources, job.context
)
cmd_line = self.command_line(job, job_dir)
log.info("Running: %s" % cmd_line)
self.job_dump(job, job_dir)
if self.container:
self.container.run(cmd_line, job_dir, env)
else:
ret = subprocess.call(['bash', '-c', cmd_line], cwd=job_dir)
if ret != 0:
raise RabixError("Command failed with exit status %s" % ret)
result_path = os.path.abspath(job_dir) + '/cwl.output.json'
if os.path.exists(result_path):
with open(result_path, 'r') as res:
outputs = json.load(res)
else:
with open(result_path, 'w') as res:
outputs = self.cli_job.get_outputs(
os.path.abspath(job_dir), abspath_job)
json.dump(job.context.to_primitive(outputs), res)
self.unmap_paths(outputs)
def write_rbx(f):
if isinstance(f, File):
with open(f.path + '.rbx.json', 'w') as rbx:
json.dump(f.to_dict(), rbx)
map_rec_collection(write_rbx, outputs)
return outputs
def run(self, job, job_dir=None):
self.load_input_content(job)
job_dir = os.path.abspath(job_dir or job.id)
if not job_dir.endswith('/'):
job_dir += '/'
if not os.path.exists(job_dir):
os.mkdir(job_dir)
os.chmod(job_dir,
os.stat(job_dir).st_mode | stat.S_IROTH | stat.S_IWOTH)
self.cli_job = CLIJob(job)
eval = ValueResolver(job)
cfr = self.get_requirement_or_hint(CreateFileRequirement)
if cfr:
cfr.create_files(job_dir, eval)
env = None
evr = self.get_requirement_or_hint(EnvVarRequirement)
if evr:
env = evr.var_map(eval)
self.ensure_files(job, job_dir)
self.install(job=job)
abspath_job = Job(job.id, job.app, copy.deepcopy(job.inputs),
job.allocated_resources, job.context)
cmd_line = self.command_line(job, job_dir)
log.info("Running: %s" % cmd_line)
self.job_dump(job, job_dir)
if self.container:
self.container.run(cmd_line, job_dir, env)
else:
ret = subprocess.call(['bash', '-c', cmd_line], cwd=job_dir)
if ret != 0:
raise RabixError("Command failed with exit status %s" % ret)
result_path = os.path.abspath(job_dir) + '/cwl.output.json'
if os.path.exists(result_path):
with open(result_path, 'r') as res:
outputs = json.load(res)
else:
with open(result_path, 'w') as res:
outputs = self.cli_job.get_outputs(os.path.abspath(job_dir),
abspath_job)
json.dump(job.context.to_primitive(outputs), res)
self.unmap_paths(outputs)
def write_rbx(f):
if isinstance(f, File):
with open(f.path + '.rbx.json', 'w') as rbx:
json.dump(f.to_dict(), rbx)
map_rec_collection(write_rbx, outputs)
return outputs
