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import logging
import gc
import os
import os.path as op
import json
from typing import List
from .blob_storage import BlobStorage, disk_usage
logger = logging.getLogger(__name__)
def generate_lineidx(filein: str, idxout: str) -> None:
idxout_tmp = idxout + '.tmp'
with open(filein, 'r') as tsvin, open(idxout_tmp, 'w') as tsvout:
fsize = os.fstat(tsvin.fileno()).st_size
fpos = 0
while fpos != fsize:
tsvout.write(str(fpos) + "\n")
tsvin.readline()
fpos = tsvin.tell()
os.rename(idxout_tmp, idxout)
def read_to_character(fp, c):
result = []
while True:
s = fp.read(32)
assert s != ''
if c in s:
result.append(s[: s.index(c)])
break
else:
result.append(s)
return ''.join(result)
class TSVFile(object):
def __init__(self,
tsv_file: str,
if_generate_lineidx: bool = True,
lineidx: str = None,
class_selector: List[str] = None,
blob_storage: BlobStorage = None):
self.tsv_file = tsv_file
self.lineidx = op.splitext(tsv_file)[0] + '.lineidx' \
if not lineidx else lineidx
self.linelist = op.splitext(tsv_file)[0] + '.linelist'
self.chunks = op.splitext(tsv_file)[0] + '.chunks'
self._fp = None
self._lineidx = None
self._sample_indices = None
self._class_boundaries = None
self._class_selector = class_selector
self._blob_storage = blob_storage
self._len = None
# the process always keeps the process which opens the file.
# If the pid is not equal to the currrent pid, we will re-open the file.
self.pid = None
# generate lineidx if not exist
if not op.isfile(self.lineidx) and if_generate_lineidx:
generate_lineidx(self.tsv_file, self.lineidx)
def __del__(self):
self.gcidx()
if self._fp:
self._fp.close()
# physically remove the tsv file if it is retrieved by BlobStorage
if self._blob_storage and 'azcopy' in self.tsv_file and os.path.exists(self.tsv_file):
try:
original_usage = disk_usage('/')
os.remove(self.tsv_file)
logger.info("Purged %s (disk usage: %.2f%% => %.2f%%)" %
(self.tsv_file, original_usage, disk_usage('/') * 100))
except:
# Known issue: multiple threads attempting to delete the file will raise a FileNotFound error.
# TODO: try Threadling.Lock to better handle the race condition
pass
def __str__(self):
return "TSVFile(tsv_file='{}')".format(self.tsv_file)
def __repr__(self):
return str(self)
def gcidx(self):
logger.debug('Run gc collect')
self._lineidx = None
self._sample_indices = None
#self._class_boundaries = None
return gc.collect()
def get_class_boundaries(self):
return self._class_boundaries
def num_rows(self, gcf=False):
if (self._len is None):
self._ensure_lineidx_loaded()
retval = len(self._sample_indices)
if (gcf):
self.gcidx()
self._len = retval
return self._len
def seek(self, idx: int):
self._ensure_tsv_opened()
self._ensure_lineidx_loaded()
try:
pos = self._lineidx[self._sample_indices[idx]]
except:
logger.info('=> {}-{}'.format(self.tsv_file, idx))
raise
self._fp.seek(pos)
return [s.strip() for s in self._fp.readline().split('\t')]
def seek_first_column(self, idx: int):
self._ensure_tsv_opened()
self._ensure_lineidx_loaded()
pos = self._lineidx[idx]
self._fp.seek(pos)
return read_to_character(self._fp, '\t')
def get_key(self, idx: int):
return self.seek_first_column(idx)
def __getitem__(self, index: int):
return self.seek(index)
def __len__(self):
return self.num_rows()
def _ensure_lineidx_loaded(self):
if self._lineidx is None:
logger.debug('=> loading lineidx: {}'.format(self.lineidx))
with open(self.lineidx, 'r') as fp:
lines = fp.readlines()
lines = [line.strip() for line in lines]
self._lineidx = [int(line) for line in lines]
# read the line list if exists
linelist = None
if op.isfile(self.linelist):
with open(self.linelist, 'r') as fp:
linelist = sorted(
[
int(line.strip())
for line in fp.readlines()
]
)
if op.isfile(self.chunks):
self._sample_indices = []
self._class_boundaries = []
class_boundaries = json.load(open(self.chunks, 'r'))
for class_name, boundary in class_boundaries.items():
start = len(self._sample_indices)
if class_name in self._class_selector:
for idx in range(boundary[0], boundary[1] + 1):
# NOTE: potentially slow when linelist is long, try to speed it up
if linelist and idx not in linelist:
continue
self._sample_indices.append(idx)
end = len(self._sample_indices)
self._class_boundaries.append((start, end))
else:
if linelist:
self._sample_indices = linelist
else:
self._sample_indices = list(range(len(self._lineidx)))
def _ensure_tsv_opened(self):
if self._fp is None:
if self._blob_storage:
self._fp = self._blob_storage.open(self.tsv_file)
else:
self._fp = open(self.tsv_file, 'r')
self.pid = os.getpid()
if self.pid != os.getpid():
logger.debug('=> re-open {} because the process id changed'.format(self.tsv_file))
self._fp = open(self.tsv_file, 'r')
self.pid = os.getpid()
class CompositeTSVFile:
def __init__(self,
file_list: List[str],
root: str = '.',
class_selector: List[str] = None,
is_train: bool = True,
sas_token_path: str = None,
azcopy_path: str = None):
self.root = root
self.tsvs = None
self.chunk_sizes = None
self.accum_chunk_sizes = None
self._class_selector = class_selector
self._class_boundaries = None
self.initialized = False
assert isinstance(file_list, list)
self.blob_storage = BlobStorage(is_train, sas_token_path, azcopy_path)
self.file_list = self.blob_storage.register_local_tsv_paths(file_list)
logger.info('=> Init CompositeTSVFile...')
self.initialize()
logger.info('=> Init CompositeTSVFile Done...')
def get_key(self, index: int):
idx_source, idx_row = self._calc_chunk_idx_row(index)
k = self.tsvs[idx_source].get_key(idx_row)
return '_'.join([self.file_list[idx_source], k])
def get_class_boundaries(self):
return self._class_boundaries
def get_chunk_size(self):
return self.chunk_sizes
def num_rows(self):
return sum(self.chunk_sizes)
def _calc_chunk_idx_row(self, index: int):
idx_chunk = 0
idx_row = index
while index >= self.accum_chunk_sizes[idx_chunk]:
idx_chunk += 1
idx_row = index - self.accum_chunk_sizes[idx_chunk-1]
return idx_chunk, idx_row
def __getitem__(self, index: int):
idx_source, idx_row = self._calc_chunk_idx_row(index)
if idx_source not in self.blob_storage:
self.blob_storage[idx_source] = TSVFile(
op.join(self.root, self.file_list[idx_source]),
class_selector=self._class_selector,
blob_storage=self.blob_storage,
if_generate_lineidx=True
)
return self.blob_storage[idx_source].seek(idx_row)
def __len__(self):
return sum(self.chunk_sizes)
def initialize(self):
"""
this function has to be called in init function if cache_policy is
enabled. Thus, let's always call it in init funciton to make it simple.
"""
if self.initialized:
return
self.tsvs = [
TSVFile(
op.join(self.root, f),
class_selector=self._class_selector
) for f in self.file_list
]
logger.debug("=> Calculating chunk sizes ...")
self.chunk_sizes = [tsv.num_rows(gcf=True) for tsv in self.tsvs]
self.accum_chunk_sizes = [0]
for size in self.chunk_sizes:
self.accum_chunk_sizes += [self.accum_chunk_sizes[-1] + size]
self.accum_chunk_sizes = self.accum_chunk_sizes[1:]
if (
self._class_selector
and all([tsv.get_class_boundaries() for tsv in self.tsvs])
):
"""
Note: When using CompositeTSVFile, make sure that the classes contained in each
tsv file do not overlap. Otherwise, the class boundaries won't be correct.
"""
self._class_boundaries = []
offset = 0
for tsv in self.tsvs:
boundaries = tsv.get_class_boundaries()
for bound in boundaries:
self._class_boundaries.append((bound[0] + offset, bound[1] + offset))
offset += len(tsv)
self.initialized = True
def load_list_file(fname: str) -> List[str]:
with open(fname, 'r') as fp:
lines = fp.readlines()
result = [line.strip() for line in lines]
if len(result) > 0 and result[-1] == '':
result = result[:-1]
return result
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