def _extract_last_nlines(path, nlines=25):
"""Attempt to extract the last nlines from a file
If the file is not found or there's an error parsing the file,
an empty string is returned.
"""
try:
n = nlines + 1
nfs_exists_check(path)
with open(path, 'r') as f:
s = f.readlines()
return "".join(s[-n:])
except Exception as e:
log.warn("Unable to extract stderr from {p}. {e}".format(p=path, e=e))
return ""
def _validate_resource(func, resource):
"""Validate the existence of a file/dir"""
_ = nfs_exists_check(resource)
if func(resource):
return os.path.abspath(resource)
else:
raise IOError("Unable to find '{f}'".format(f=resource))
def _validate_resource(func, resource):
"""Validate the existence of a file/dir"""
_ = nfs_exists_check(resource)
if func(resource):
return os.path.abspath(resource)
else:
raise IOError("Unable to find '{f}'".format(f=resource))
def fofn_to_files(fofn):
"""Util func to convert a bas/bax fofn file to a list of bas/bax files."""
_ = nfs_exists_check(fofn)
if os.path.exists(fofn):
with open(fofn, 'r') as f:
bas_files = {line.strip() for line in f.readlines()}
for bas_file in bas_files:
if not os.path.isfile(bas_file):
# try one more time to find the file by
# performing an NFS refresh
found = nfs_exists_check(bas_file)
if not found:
raise IOError("Unable to find bas/bax file '{f}'".format(f=bas_file))
return list(bas_files)
else:
raise IOError("Unable to find FOFN {f}".format(f=fofn))
def fofn_to_files(fofn):
"""Util func to convert a bas/bax fofn file to a list of bas/bax files."""
_ = nfs_exists_check(fofn)
if os.path.exists(fofn):
with open(fofn, 'r') as f:
bas_files = {line.strip() for line in f.readlines()}
for bas_file in bas_files:
if not os.path.isfile(bas_file):
# try one more time to find the file by
# performing an NFS refresh
found = nfs_exists_check(bas_file)
if not found:
raise IOError("Unable to find bas/bax file '{f}'".format(f=bas_file))
return list(bas_files)
else:
raise IOError("Unable to find FOFN {f}".format(f=fofn))
def validate_fofn(fofn):
"""Validate existence of FOFN and files within the FOFN.
:param fofn: (str) Path to File of file names.
:raises: IOError if any file is not found.
:return: (str) abspath of the input fofn
"""
_ = nfs_exists_check(fofn)
if os.path.isfile(fofn):
file_names = fofn_to_files(os.path.abspath(fofn))
log.debug("Found {n} files in FOFN {f}.".format(n=len(file_names), f=fofn))
return os.path.abspath(fofn)
else:
raise IOError("Unable to find {f}".format(f=fofn))
def validate_fofn(fofn):
"""Validate existence of FOFN and files within the FOFN.
:param fofn: (str) Path to File of file names.
:raises: IOError if any file is not found.
:return: (str) abspath of the input fofn
"""
_ = nfs_exists_check(fofn)
if os.path.isfile(fofn):
file_names = fofn_to_files(os.path.abspath(fofn))
log.debug("Found {n} files in FOFN {f}.".format(n=len(file_names), f=fofn))
return os.path.abspath(fofn)
else:
raise IOError("Unable to find {f}".format(f=fofn))
def trigger_nfs_refresh(ff):
# keeping this for backward compatibility
return nfs_exists_check(ff)
def trigger_nfs_refresh(ff):
# keeping this for backward compatibility
return nfs_exists_check(ff)
