def convert(cls, filepath, other_file, buffersize=None, library=None):
"""Instantiate a BaseFile object from another
BaseFile object.
"""
if not isinstance(other_file, BaseFile):
raise CancerApiException("Must pass cancer_api file object as `other_file`.")
obj = cls._init(filepath=filepath, parser_cls=None, other_file=other_file, is_new=True,
buffersize=buffersize, library=library)
obj.write()
return obj
def add_obj(self, obj):
"""Add object to storelist. Useful to bind objects
to files created with the `new` constructor.
Returns whether the object was added
(always True for now).
"""
if not isinstance(obj, CancerApiObject):
raise CancerApiException("`add_obj` only supports cancer_api objects")
self.storelist.append(obj)
if self.buffersize and len(self.storelist) >= self.buffersize:
self.write()
return True
def write(self, outfilepath=None, mode="w"):
"""Write objects in file to disk.
Either you can write to a new file (if outfilepath is given),
or you can append what's in storelist to the current filepath.
"""
# If outfilepath is specified, iterate over every object in self
# (which might come from something else) and every object in
# self.storelist and write them out to disk
if outfilepath:
with open_file(outfilepath, mode) as outfile:
logging.info("Writing to disk...")
outfile.write(self.get_header())
for obj in self.source:
line = self.obj_to_str(obj)
outfile.write(line)
for obj in self.storelist:
line = self.obj_to_str(obj)
outfile.write(line)
# Clear storelist now that they've been written to disk
self.clear_storelist()
# Update file attributes (in case of new or converted file)
self.source = self
self.filepath = outfilepath
self.is_new = False
# If outfilepath is not specified, simply iterate over every
# object in self.storelist and append them to the file on disk.
else:
# If the file is new and the path already exist, do not append
if self.is_new and os.path.exists(self.filepath):
raise CancerApiException(
"Output file already exists: {}".format(self.filepath))
with open_file(self.filepath, "a+") as outfile:
logging.info("Writing to disk...")
# If the file is new, start with header
if self.is_new:
outfile.write(self.get_header())
# If file is new and source is not self (i.e., converted file),
# iterate over source
if self.is_new and self.source is not self:
for obj in self.source:
line = self.obj_to_str(obj)
outfile.write(line)
# Proceed with iterating over storelist
for obj in self.storelist:
line = self.obj_to_str(obj)
outfile.write(line)
# Clear storelist now that they've been written to disk
self.clear_storelist()
# Update file attributes (in case of new or converted file)
self.source = self
self.is_new = False
def __init__(self, *args, **kwargs):
"""Can't initialize directly."""
raise CancerApiException(
"Please use `open`, `convert` or `new` methods instead.")