def partially_expand(f, wildcards):
"""Expand the wildcards in f from the ones present in wildcards
This is done by replacing all wildcard delimiters by `{{` or `}}`
that are not in `wildcards.keys()`.
"""
# perform the partial expansion from f's string representation
s = str(f).replace("{", "{{").replace("}", "}}")
for key in wildcards.keys():
s = s.replace("{{{{{}}}}}".format(key), "{{{}}}".format(key))
# build result
anno_s = AnnotatedString(s)
anno_s.flags = f.flags
return IOFile(anno_s, f.rule)
def partially_expand(f, wildcards):
"""Expand the wildcards in f from the ones present in wildcards
This is done by replacing all wildcard delimiters by `{{` or `}}`
that are not in `wildcards.keys()`.
"""
# perform the partial expansion from f's string representation
s = str(f).replace('{', '{{').replace('}', '}}')
for key in wildcards.keys():
s = s.replace('{{{{{}}}}}'.format(key),
'{{{}}}'.format(key))
# build result
anno_s = AnnotatedString(s)
anno_s.flags = f.flags
return IOFile(anno_s, f.rule)
def modify(self, path, property=None):
modified_path = self.apply_default_remote(self.replace_prefix(path, property))
# Important, update with previous flags in case of AnnotatedString #596
if hasattr(path, "flags"):
if not hasattr(modified_path, "flags"):
modified_path = AnnotatedString(modified_path)
modified_path.flags.update(path.flags)
return modified_path
def format_annotated(self, item, expand_args):
"""Wrapper for :meth:format preserving *AnnotatedString* flags
Calls :meth:format to format *item* into a new string and copies
flags from original item.
This is used by :meth:expand
"""
updated = self.format(item, **expand_args)
if isinstance(item, AnnotatedString):
updated = AnnotatedString(updated)
try:
updated.flags = deepcopy(item.flags)
except TypeError:
log.debug("Failed to deepcopy flags for item {} with flags{}"
"".format(item, item.flags))
updated.flags = copy(item.flags)
return updated
def cleanup(f):
prefix = self.rule.workflow.default_remote_prefix
# remove constraints and turn this into a plain string
cleaned = strip_wildcard_constraints(f)
if (self.rule.workflow.default_remote_provider is not None
and f.startswith(prefix) and not is_flagged(f, "local")):
cleaned = f[len(prefix) + 1:]
cleaned = IOFile(cleaned, rule=self.rule)
else:
cleaned = IOFile(AnnotatedString(cleaned), rule=self.rule)
cleaned.clone_remote_object(f)
return cleaned
def modify(self, path, property=None):
if get_flag_value(path, PATH_MODIFIER_FLAG) is self:
# Path has been modified before and is reused now, no need to modify again.
return path
modified_path = self.apply_default_remote(
self.replace_prefix(path, property))
if modified_path == path:
# nothing has changed
return path
# Important, update with previous flags in case of AnnotatedString #596
if hasattr(path, "flags"):
if not hasattr(modified_path, "flags"):
modified_path = AnnotatedString(modified_path)
modified_path.flags.update(path.flags)
if is_flagged(modified_path, "multiext"):
modified_path.flags["multiext"] = self.apply_default_remote(
self.replace_prefix(modified_path.flags["multiext"],
property))
# Flag the path as modified and return.
modified_path = flag(modified_path, PATH_MODIFIER_FLAG, self)
return modified_path
def expand(self, item, fields, rec=-1):
if isinstance(item, str):
updated = self.format(item, **fields)
if isinstance(item, AnnotatedString):
updated = AnnotatedString(updated)
try:
updated.flags = deepcopy(item.flags)
except TypeError as e:
log.debug(
"Failed to deepcopy flags for item {} with flags{}"
"".format(item, item.flags))
updated.flags = copy(item.flags)
item = updated
elif hasattr(item, '__call__'): # function
_item = item
def late_expand(*args, **kwargs):
return self.expand(_item(*args, **kwargs), {'wc': args[0]},
rec=rec + 1)
item = late_expand
elif isinstance(item, int):
pass
elif isinstance(item, dict):
for key, value in item.items():
item[key] = self.expand(value, fields, rec=rec + 1)
elif isinstance(item, list):
for i, subitem in enumerate(item):
item[i] = self.expand(subitem, fields, rec=rec + 1)
elif isinstance(item, tuple):
return (self.expand(subitem, fields, rec=rec + 1)
for subitem in item)
else:
raise ValueError("unable to expand item '{}' with fields '{}'"
"".format(repr(item), repr(fields)))
return item
def cleanup(f):
prefix = self.rule.workflow.default_remote_prefix
# remove constraints and turn this into a plain string
cleaned = strip_wildcard_constraints(f)
modified_by = get_flag_value(f, PATH_MODIFIER_FLAG)
if (self.rule.workflow.default_remote_provider is not None
and f.startswith(prefix) and not is_flagged(f, "local")):
cleaned = f[len(prefix) + 1:]
cleaned = IOFile(cleaned, rule=self.rule)
else:
cleaned = IOFile(AnnotatedString(cleaned), rule=self.rule)
cleaned.clone_remote_object(f)
if modified_by is not None:
cleaned.flags[PATH_MODIFIER_FLAG] = modified_by
return cleaned
