import csv import io import itertools import json import re from collections import defaultdict import conllu from chardet import UniversalDetector from django.db import transaction from django.conf import settings from colour import Color import pyexcel from rest_framework.renderers import JSONRenderer from seqeval.metrics.sequence_labeling import get_entities from .exceptions import FileParseException from .models import Label from .serializers import DocumentSerializer, LabelSerializer def extract_label(tag): ptn = re.compile(r'(B|I|E|S)-(.+)') m = ptn.match(tag) if m: return m.groups()[1] else: return tag class BaseStorage(object): def __init__(self, data, project): self.data = data self.project = project @transaction.atomic def save(self, user): raise NotImplementedError() def save_doc(self, data): serializer = DocumentSerializer(data=data, many=True) serializer.is_valid(raise_exception=True) doc = serializer.save(project=self.project) return doc def save_label(self, data): serializer = LabelSerializer(data=data, many=True) serializer.is_valid(raise_exception=True) label = serializer.save(project=self.project) return label def save_annotation(self, data, user): annotation_serializer = self.project.get_annotation_serializer() serializer = annotation_serializer(data=data, many=True) serializer.is_valid(raise_exception=True) annotation = serializer.save(user=user) return annotation @classmethod def extract_label(cls, data): return [d.get('labels', []) for d in data] @classmethod def exclude_created_labels(cls, labels, created): return [label for label in labels if label not in created] @classmethod def to_serializer_format(cls, labels, created): existing_shortkeys = {(label.suffix_key, label.prefix_key) for label in created.values()} serializer_labels = [] for label in sorted(labels): serializer_label = {'text': label} shortkey = cls.get_shortkey(label, existing_shortkeys) if shortkey: serializer_label['suffix_key'] = shortkey[0] serializer_label['prefix_key'] = shortkey[1] existing_shortkeys.add(shortkey) background_color = Color(pick_for=label) text_color = Color('white') if background_color.get_luminance() < 0.5 else Color('black') serializer_label['background_color'] = background_color.hex serializer_label['text_color'] = text_color.hex serializer_labels.append(serializer_label) return serializer_labels @classmethod def get_shortkey(cls, label, existing_shortkeys): model_prefix_keys = [key for (key, _) in Label.PREFIX_KEYS] prefix_keys = [None] + model_prefix_keys model_suffix_keys = {key for (key, _) in Label.SUFFIX_KEYS} suffix_keys = [key for key in label.lower() if key in model_suffix_keys] for shortkey in itertools.product(suffix_keys, prefix_keys): if shortkey not in existing_shortkeys: return shortkey return None @classmethod def update_saved_labels(cls, saved, new): for label in new: saved[label.text] = label return saved class PlainStorage(BaseStorage): @transaction.atomic def save(self, user): for text in self.data: self.save_doc(text) class ClassificationStorage(BaseStorage): """Store json for text classification. The format is as follows: {"text": "Python is awesome!", "labels": ["positive"]} ... """ @transaction.atomic def save(self, user): saved_labels = {label.text: label for label in self.project.labels.all()} for data in self.data: docs = self.save_doc(data) labels = self.extract_label(data) unique_labels = self.extract_unique_labels(labels) unique_labels = self.exclude_created_labels(unique_labels, saved_labels) unique_labels = self.to_serializer_format(unique_labels, saved_labels) new_labels = self.save_label(unique_labels) saved_labels = self.update_saved_labels(saved_labels, new_labels) annotations = self.make_annotations(docs, labels, saved_labels) self.save_annotation(annotations, user) @classmethod def extract_unique_labels(cls, labels): return set(itertools.chain(*labels)) @classmethod def make_annotations(cls, docs, labels, saved_labels): annotations = [] for doc, label in zip(docs, labels): for name in label: label = saved_labels[name] annotations.append({'document': doc.id, 'label': label.id}) return annotations class SequenceLabelingStorage(BaseStorage): """Upload jsonl for sequence labeling. The format is as follows: {"text": "Python is awesome!", "labels": [[0, 6, "Product"],]} ... """ @transaction.atomic def save(self, user): saved_labels = {label.text: label for label in self.project.labels.all()} for data in self.data: docs = self.save_doc(data) labels = self.extract_label(data) unique_labels = self.extract_unique_labels(labels) unique_labels = self.exclude_created_labels(unique_labels, saved_labels) unique_labels = self.to_serializer_format(unique_labels, saved_labels) new_labels = self.save_label(unique_labels) saved_labels = self.update_saved_labels(saved_labels, new_labels) annotations = self.make_annotations(docs, labels, saved_labels) self.save_annotation(annotations, user) @classmethod def extract_unique_labels(cls, labels): return set([label for _, _, label in itertools.chain(*labels)]) @classmethod def make_annotations(cls, docs, labels, saved_labels): annotations = [] for doc, spans in zip(docs, labels): for span in spans: start_offset, end_offset, name = span label = saved_labels[name] annotations.append({'document': doc.id, 'label': label.id, 'start_offset': start_offset, 'end_offset': end_offset}) return annotations class Seq2seqStorage(BaseStorage): """Store json for seq2seq. The format is as follows: {"text": "Hello, World!", "labels": ["こんにちは、世界!"]} ... """ @transaction.atomic def save(self, user): for data in self.data: doc = self.save_doc(data) labels = self.extract_label(data) annotations = self.make_annotations(doc, labels) self.save_annotation(annotations, user) @classmethod def make_annotations(cls, docs, labels): annotations = [] for doc, texts in zip(docs, labels): for text in texts: annotations.append({'document': doc.id, 'text': text}) return annotations class FileParser(object): def parse(self, file): raise NotImplementedError() @staticmethod def encode_metadata(data): return json.dumps(data, ensure_ascii=False) class CoNLLParser(FileParser): """Uploads CoNLL format file. The file format is tab-separated values. A blank line is required at the end of a sentence. For example: ``` EU B-ORG rejects O German B-MISC call O to O boycott O British B-MISC lamb O . O Peter B-PER Blackburn I-PER ... ``` """ def parse(self, file): data = [] file = EncodedIO(file) file = io.TextIOWrapper(file, encoding=file.encoding) # Add check exception field_parsers = { "ne": lambda line, i: conllu.parser.parse_nullable_value(line[i]), } gen_parser = conllu.parse_incr( file, fields=("form", "ne"), field_parsers=field_parsers ) try: for sentence in gen_parser: if not sentence: continue if len(data) >= settings.IMPORT_BATCH_SIZE: yield data data = [] words, labels = [], [] for item in sentence: word = item.get("form") tag = item.get("ne") if tag is not None: char_left = sum(map(len, words)) + len(words) char_right = char_left + len(word) span = [char_left, char_right, tag] labels.append(span) words.append(word) # Create and add JSONL data.append({'text': ' '.join(words), 'labels': labels}) except conllu.parser.ParseException as e: raise FileParseException(line_num=-1, line=str(e)) if data: yield data class PlainTextParser(FileParser): """Uploads plain text. The file format is as follows: ``` EU rejects German call to boycott British lamb. President Obama is speaking at the White House. ... ``` """ def parse(self, file): file = EncodedIO(file) file = io.TextIOWrapper(file, encoding=file.encoding) while True: batch = list(itertools.islice(file, settings.IMPORT_BATCH_SIZE)) if not batch: break yield [{'text': line.strip()} for line in batch] class CSVParser(FileParser): """Uploads csv file. The file format is comma separated values. Column names are required at the top of a file. For example: ``` text, label "EU rejects German call to boycott British lamb.",Politics "President Obama is speaking at the White House.",Politics "He lives in Newark, Ohio.",Other ... ``` """ def parse(self, file): file = EncodedIO(file) file = io.TextIOWrapper(file, encoding=file.encoding) reader = csv.reader(file) yield from ExcelParser.parse_excel_csv_reader(reader) class ExcelParser(FileParser): def parse(self, file): excel_book = pyexcel.iget_book(file_type="xlsx", file_content=file.read()) # Handle multiple sheets for sheet_name in excel_book.sheet_names(): reader = excel_book[sheet_name].to_array() yield from self.parse_excel_csv_reader(reader) @staticmethod def parse_excel_csv_reader(reader): columns = next(reader) data = [] if len(columns) == 1 and columns[0] != 'text': data.append({'text': columns[0]}) for i, row in enumerate(reader, start=2): if len(data) >= settings.IMPORT_BATCH_SIZE: yield data data = [] # Only text column if len(row) == len(columns) and len(row) == 1: data.append({'text': row[0]}) # Text, labels and metadata columns elif len(row) == len(columns) and len(row) >= 2: datum = dict(zip(columns, row)) text, label = datum.pop('text'), datum.pop('label') meta = FileParser.encode_metadata(datum) j = {'text': text, 'labels': [label], 'meta': meta} data.append(j) else: raise FileParseException(line_num=i, line=row) if data: yield data class JSONParser(FileParser): def parse(self, file): file = EncodedIO(file) file = io.TextIOWrapper(file, encoding=file.encoding) data = [] for i, line in enumerate(file, start=1): if len(data) >= settings.IMPORT_BATCH_SIZE: yield data data = [] try: j = json.loads(line) j['meta'] = FileParser.encode_metadata(j.get('meta', {})) data.append(j) except json.decoder.JSONDecodeError: raise FileParseException(line_num=i, line=line) if data: yield data class JSONLRenderer(JSONRenderer): def render(self, data, accepted_media_type=None, renderer_context=None): """ Render `data` into JSON, returning a bytestring. """ if data is None: return bytes() if not isinstance(data, list): data = [data] for d in data: yield json.dumps(d, cls=self.encoder_class, ensure_ascii=self.ensure_ascii, allow_nan=not self.strict) + '\n' class JSONPainter(object): def paint(self, documents): serializer = DocumentSerializer(documents, many=True) data = [] for d in serializer.data: d['meta'] = json.loads(d['meta']) for a in d['annotations']: a.pop('id') a.pop('prob') a.pop('document') data.append(d) return data @staticmethod def paint_labels(documents, labels): serializer_labels = LabelSerializer(labels, many=True) serializer = DocumentSerializer(documents, many=True) data = [] for d in serializer.data: labels = [] for a in d['annotations']: label_obj = [x for x in serializer_labels.data if x['id'] == a['label']][0] label_text = label_obj['text'] label_start = a['start_offset'] label_end = a['end_offset'] labels.append([label_start, label_end, label_text]) d.pop('annotations') d['labels'] = labels d['meta'] = json.loads(d['meta']) data.append(d) return data class CSVPainter(JSONPainter): def paint(self, documents): data = super().paint(documents) res = [] for d in data: annotations = d.pop('annotations') for a in annotations: res.append({**d, **a}) return res def iterable_to_io(iterable, buffer_size=io.DEFAULT_BUFFER_SIZE): """See https://stackoverflow.com/a/20260030/3817588.""" class IterStream(io.RawIOBase): def __init__(self): self.leftover = None def readable(self): return True def readinto(self, b): try: l = len(b) # We're supposed to return at most this much chunk = self.leftover or next(iterable) output, self.leftover = chunk[:l], chunk[l:] b[:len(output)] = output return len(output) except StopIteration: return 0 # indicate EOF return io.BufferedReader(IterStream(), buffer_size=buffer_size) class EncodedIO(io.RawIOBase): def __init__(self, fobj, buffer_size=io.DEFAULT_BUFFER_SIZE, default_encoding='utf-8'): buffer = b'' detector = UniversalDetector() while True: read = fobj.read(buffer_size) detector.feed(read) buffer += read if detector.done or len(read) < buffer_size: break if detector.done: self.encoding = detector.result['encoding'] else: self.encoding = default_encoding self._fobj = fobj self._buffer = buffer def readable(self): return self._fobj.readable() def readinto(self, b): l = len(b) chunk = self._buffer or self._fobj.read(l) output, self._buffer = chunk[:l], chunk[l:] b[:len(output)] = output return len(output)