def _needs_liftover(self, from_assembly, to_assembly, newfile):
# Sentinel file encodes
sentinel = self._liftover_sentinel(from_assembly, to_assembly, newfile)
if not os.path.exists(sentinel):
return True
elif utils.is_newer(self.processed, newfile):
return True
return False
def _needs_liftover(self, from_assembly, to_assembly, newfile):
# Sentinel file encodes
sentinel = self._liftover_sentinel(from_assembly, to_assembly, newfile)
if not os.path.exists(sentinel):
return True
elif utils.is_newer(self.processed, newfile):
return True
return False
def _needs_liftover(self, from_assembly, to_assembly, newfile):
"""
Checks to see if liftover is needed based on the
"""
# Sentinel file encodes assembly conversion;
sentinel = self._liftover_sentinel(from_assembly, to_assembly, newfile)
if not os.path.exists(sentinel):
return True
elif utils.is_newer(self.processed, newfile):
return True
return False
def _needs_update(self):
"""
Decides if we need to update the processed file.
"""
do_update = False
if self._was_lifted_over():
log(
"This file appears to have been lifted over from another "
"study, in which case we assume it does not need updating",
style=Fore.YELLOW
)
return False
if self._needs_download():
log("{0.original} does not exist; downloading"
.format(self, indent=4))
self._download()
do_update = True
if not os.path.exists(self.processed):
log("{0.processed} does not exist".format(self), indent=4)
do_update = True
# if processed is a link, then check the LINK time
if (
os.path.exists(self.processed) and
utils.link_is_newer(self.script, self.processed)
):
log("{0.script} is newer than {0.processed}, need to re-run"
.format(self), indent=4)
do_update = True
# but for the original data, we want to FOLLOW the link
if (
os.path.exists(self.original) and
os.path.exists(self.processed) and
utils.is_newer(self.original, self.processed)
):
log("{0.original} is newer than {0.processed}, need to re-run"
.format(self), indent=4)
do_update = True
if not do_update:
log("{0.processed} is up to date"
.format(self), indent=4, style=Style.DIM)
return do_update
def _needs_update(self):
"""
Decides if we need to update the processed file.
"""
do_update = False
if self._was_lifted_over():
log(
"This file appears to have been lifted over from another "
"study, in which case we assume it does not need updating",
style=Fore.YELLOW)
return False
if self._needs_download():
log("{0.original} does not exist; downloading".format(self,
indent=4))
self._download()
do_update = True
if not os.path.exists(self.processed):
log("{0.processed} does not exist".format(self), indent=4)
do_update = True
# if processed is a link, then check the LINK time
if (os.path.exists(self.processed)
and utils.link_is_newer(self.script, self.processed)):
log("{0.script} is newer than {0.processed}, need to re-run".
format(self),
indent=4)
do_update = True
# but for the original data, we want to FOLLOW the link
if (os.path.exists(self.original) and os.path.exists(self.processed)
and utils.is_newer(self.original, self.processed)):
log("{0.original} is newer than {0.processed}, need to re-run".
format(self),
indent=4)
do_update = True
if not do_update:
log("{0.processed} is up to date".format(self),
indent=4,
style=Style.DIM)
return do_update
