def commands(self):
rel_exe_dir = relpath(abspath(self.exe_dir), abspath(self.modelpath))
copy_input_to_scratch, copy_input_to_exe_dir = self.copy_input()
return template(copy_hawc2=self.copy_hawc2(),
exe_dir=cluster_path(self.exe_dir),
copy_input_to_scratch=copy_input_to_scratch,
copy_input_to_exe_dir=copy_input_to_exe_dir,
rel_exe_dir=rel_exe_dir,
hawc2_cmd=self.hawc2_cmd,
htc_file=self.htc_file,
jobname=self.jobname,
copy_output=self.copy_output(),
modelpath=cluster_path(self.modelpath),
modelname=self.modelname)
def auto_detect_modelpath(self):
if self.filename is None:
return "../"
#print (["../"*i for i in range(3)])
import numpy as np
input_files = HTCFile(self.filename, 'unknown').input_files()
if len(input_files) == 1: # only input file is the htc file
return "../"
rel_input_files = [f for f in input_files if not os.path.isabs(f)]
def isfile_case_insensitive(f):
try:
f = fixcase(f) # raises exception if not existing
return os.path.isfile(f)
except IOError:
return False
found = ([np.sum([isfile_case_insensitive(os.path.join(os.path.dirname(self.filename), "../" * i, f))
for f in rel_input_files]) for i in range(4)])
if max(found) > 0:
relpath = "../" * np.argmax(found)
return abspath(pjoin(os.path.dirname(self.filename), relpath))
else:
raise ValueError(
"Modelpath cannot be autodetected for '%s'.\nInput files not found near htc file" % self.filename)
def __init__(self, filename=None, modelpath=None, jinja_tags={}):
"""
Parameters
---------
filename : str
Absolute filename of htc file
modelpath : str
Model path relative to htc file
"""
if filename is not None:
try:
filename = fixcase(abspath(filename))
with self.open(str(filename)):
pass
except Exception:
pass
self.filename = filename
self.jinja_tags = jinja_tags
self.modelpath = modelpath or self.auto_detect_modelpath()
if filename and self.modelpath != "unknown" and not os.path.isabs(self.modelpath):
drive, p = os.path.splitdrive(os.path.join(os.path.dirname(str(self.filename)), self.modelpath))
self.modelpath = os.path.join(drive, os.path.splitdrive(os.path.realpath(p))[1]).replace("\\", "/")
if self.modelpath != 'unknown' and self.modelpath[-1] != '/':
self.modelpath += "/"
def __init__(self, hawc2_path, hawc2_cmd, htc_file, exe_dir, input_files, output_files, queue='workq', walltime='00:10:00'):
self.hawc2_path = hawc2_path
self.hawc2_cmd = hawc2_cmd
self.htc_file = htc_file
self.exe_dir = exe_dir
self.queue = queue
self.walltime = walltime
if not os.path.isabs(htc_file):
htc_file = pjoin(exe_dir, htc_file)
else:
htc_file = htc_file.replace("\\", "/")
if htc_file not in input_files:
input_files.append(htc_file)
self.input_files = [abspath((pjoin(exe_dir, f), abspath(f))[os.path.isabs(f)])
for f in input_files]
self.htc_file = relpath(htc_file, exe_dir)
self.output_files = [abspath((pjoin(exe_dir, f), abspath(f))[os.path.isabs(f)])
for f in output_files]
self.model_path = abspath(pjoin(exe_dir, relpath(os.path.commonprefix(
self.input_files + self.output_files).rpartition("/")[0], exe_dir)))
self.model_name = os.path.basename(abspath(self.model_path))
self.jobname = os.path.splitext(os.path.basename(htc_file))[0]
PBSFile.__init__(self, self.model_path, self.jobname, self.commands, queue, walltime=walltime)