Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/boltons/jsonutils.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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# -*- coding: utf-8 -*- """``jsonutils`` aims to provide various helpers for working with JSON. Currently it focuses on providing a reliable and intuitive means of working with `JSON Lines`_-formatted files. .. _JSON Lines: http://jsonlines.org/ """ from __future__ import print_function import os import json DEFAULT_BLOCKSIZE = 4096 # reverse iter lines algorithm: # # - if it ends in a newline, add an empty string to the line list # - if there's one item, then prepend it to the buffer, continue # - if there's more than one item, pop the last item and prepend it # to the buffer, yielding it # - yield all remaining items in reverse, except for the first # - first item becomes the new buffer # # - when the outer loop completes, yield the buffer __all__ = ['JSONLIterator', 'reverse_iter_lines'] def reverse_iter_lines(file_obj, blocksize=DEFAULT_BLOCKSIZE, preseek=True): """Returns an iterator over the lines from a file object, in reverse order, i.e., last line first, first line last. Uses the :meth:`file.seek` method of file objects, and is tested compatible with :class:`file` objects, as well as :class:`StringIO.StringIO`. Args: file_obj (file): An open file object. Note that ``reverse_iter_lines`` mutably reads from the file and other functions should not mutably interact with the file object. blocksize (int): The block size to pass to :meth:`file.read()` preseek (bool): Tells the function whether or not to automatically seek to the end of the file. Defaults to ``True``. ``preseek=False`` is useful in cases when the file cursor is already in position, either at the end of the file or in the middle for relative reverse line generation. """ if preseek: file_obj.seek(0, os.SEEK_END) cur_pos = file_obj.tell() buff = '' while 0 < cur_pos: read_size = min(blocksize, cur_pos) cur_pos -= read_size file_obj.seek(cur_pos, os.SEEK_SET) cur = file_obj.read(read_size) lines = cur.splitlines() if cur[-1] == '\n': lines.append('') if len(lines) == 1: buff = lines[0] + buff continue last = lines.pop() yield last + buff for line in lines[:0:-1]: yield line buff = lines[0] if buff: # TODO: test this, does an empty buffer always mean don't yield? yield buff """ TODO: allow passthroughs for: json.load(fp[, encoding[, cls[, object_hook[, parse_float[, parse_int[, parse_constant[, object_pairs_hook[, **kw]]]]]]]]) """ class JSONLIterator(object): """The ``JSONLIterator`` is used to iterate over JSON-encoded objects stored in the `JSON Lines format`_ (one object per line). Most notably it has the ability to efficiently read from the bottom of files, making it very effective for reading in simple append-only JSONL use cases. It also has the ability to start from anywhere in the file and ignore corrupted lines. Args: file_obj (file): An open file object. ignore_errors (bool): Whether to skip over lines that raise an error on deserialization (:func:`json.loads`). reverse (bool): Controls the direction of the iteration. Defaults to ``False``. If set to ``True`` and *rel_seek* is unset, seeks to the end of the file before iteration begins. rel_seek (float): Used to preseek the start position of iteration. Set to 0.0 for the start of the file, 1.0 for the end, and anything in between. .. _JSON Lines format: http://jsonlines.org/ """ def __init__(self, file_obj, ignore_errors=False, reverse=False, rel_seek=None): self._reverse = bool(reverse) self._file_obj = file_obj self.ignore_errors = ignore_errors if rel_seek is None: if reverse: rel_seek = 1.0 elif not -1.0 < rel_seek < 1.0: raise ValueError("'rel_seek' expected a float between" " -1.0 and 1.0, not %r" % rel_seek) elif rel_seek < 0: rel_seek = 1.0 - rel_seek self._rel_seek = rel_seek self._blocksize = 4096 if rel_seek is not None: self._init_rel_seek() if self._reverse: self._line_iter = reverse_iter_lines(self._file_obj, blocksize=self._blocksize, preseek=False) else: self._line_iter = iter(self._file_obj) @property def cur_byte_pos(self): "A property representing where in the file the iterator is reading." return self._file_obj.tell() def _align_to_newline(self): "Aligns the file object's position to the next newline." fo, bsize = self._file_obj, self._blocksize cur, total_read = '', 0 cur_pos = fo.tell() while '\n' not in cur: cur = fo.read(bsize) total_read += bsize try: newline_offset = cur.index('\n') + total_read - bsize except ValueError: raise # TODO: seek to end? fo.seek(cur_pos + newline_offset) def _init_rel_seek(self): "Sets the file object's position to the relative location set above." rs, fo = self._rel_seek, self._file_obj if rs == 0.0: fo.seek(0, os.SEEK_SET) else: fo.seek(0, os.SEEK_END) size = fo.tell() if rs == 1.0: self._cur_pos = size else: target = int(size * rs) fo.seek(target, os.SEEK_SET) self._align_to_newline() self._cur_pos = fo.tell() def __iter__(self): return self def next(self): """Yields one :class:`dict` loaded with :func:`json.loads`, advancing the file object by one line. Raises :exc:`StopIteration` upon reaching the end of the file (or beginning, if ``reverse`` was set to ``True``. """ while 1: line = next(self._line_iter).lstrip() if not line: continue try: obj = json.loads(line) except Exception: if not self.ignore_errors: raise continue return obj __next__ = next if __name__ == '__main__': def _main(): import sys if '-h' in sys.argv or '--help' in sys.argv: print('loads one or more JSON Line files for basic validation.') return verbose = False if '-v' in sys.argv or '--verbose' in sys.argv: verbose = True file_count, obj_count = 0, 0 filenames = sys.argv[1:] for filename in filenames: if filename in ('-h', '--help', '-v', '--verbose'): continue file_count += 1 with open(filename, 'rb') as file_obj: iterator = JSONLIterator(file_obj) cur_obj_count = 0 while 1: try: next(iterator) except ValueError: print('error reading object #%s around byte %s in %s' % (cur_obj_count + 1, iterator.cur_byte_pos, filename)) return except StopIteration: break obj_count += 1 cur_obj_count += 1 if verbose and obj_count and obj_count % 100 == 0: sys.stdout.write('.') if obj_count % 10000: sys.stdout.write('%s\n' % obj_count) if verbose: print('files checked: %s' % file_count) print('objects loaded: %s' % obj_count) return _main()