Exemple #1
0
 def __init__(self):
     print(os.path.join(self.SETTINGS_DIR, 'corpus.json'))
     f = open(os.path.join(self.SETTINGS_DIR, 'corpus.json'),
              'r', encoding='utf-8')
     self.settings = json.loads(f.read())
     f.close()
     self.name = self.settings['corpus_name']
     self.languages = self.settings['languages']
     if len(self.languages) <= 0:
         self.languages = [self.name]
     self.input_format = self.settings['input_format']
     self.corpus_dir = os.path.join('../corpus', self.name)
     self.iterSent = None
     if self.input_format in ['json', 'json-gzip']:
         self.iterSent = JSONDocReader(format=self.input_format)
     self.goodWordFields = ['lex', 'wf', 'wf_display',
                            'parts', 'gloss', 'gloss_index', 'n_ana',
                            'trans_en', 'trans_ru']
     self.AdditionalWordFields = set()
     if 'word_fields' in self.settings:
         self.AdditionalWordFields |= set(self.settings['word_fields'])
     if 'word_table_fields' in self.settings:
         self.AdditionalWordFields |= set(self.settings['word_table_fields'])
     if 'accidental_word_fields' in self.settings:
         self.AdditionalWordFields -= set(self.settings['accidental_word_fields'])
     f = open(os.path.join(self.SETTINGS_DIR, 'categories.json'),
              'r', encoding='utf-8')
     categories = json.loads(f.read())
     self.goodWordFields += ['gr.' + v for lang in categories
                             for v in categories[lang].values()]
     self.goodWordFields = set(self.goodWordFields)
     f.close()
     self.pd = PrepareData()
     self.es = Elasticsearch()
     self.es_ic = IndicesClient(self.es)
     self.shuffled_ids = [i for i in range(1, 1000000)]
     random.shuffle(self.shuffled_ids)
     self.shuffled_ids.insert(0, 0)    # id=0 is special and should not change
     self.tmpWordIDs = [{} for i in range(len(self.languages))]    # word as JSON -> its integer ID
     self.tmpLemmaIDs = [{} for i in range(len(self.languages))]   # lemma as string -> its integer ID
     self.word2lemma = [{} for i in range(len(self.languages))]    # word's ID -> ID of its lemma (or -1, if none)
     self.wordFreqs = [{} for i in range(len(self.languages))]     # word's ID -> its frequency
     self.wordSFreqs = [{} for i in range(len(self.languages))]    # word's ID -> its number of sentences
     self.wordDocFreqs = [{} for i in range(len(self.languages))]  # (word's ID, dID) -> word frequency in the document
     # self.wordSIDs = [{} for i in range(len(self.languages))]      # word's ID -> set of sentence IDs
     self.wordDIDs = [{} for i in range(len(self.languages))]      # word's ID -> set of document IDs
     self.wfs = set()         # set of word forms (for sorting)
     self.lemmata = set()     # set of lemmata (for sorting)
     self.sID = 0          # current sentence ID for each language
     self.dID = 0          # current document ID
     self.wID = 0          # current word ID
     self.wordFreqID = 0
     self.numWords = 0     # number of words in current document
     self.numSents = 0     # number of sentences in current document
     self.numWordsLang = [0] * len(self.languages)    # number of words in each language in current document
     self.numSentsLang = [0] * len(self.languages)    # number of sentences in each language in current document
     self.totalNumWords = 0
Exemple #2
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def init():
    prepare_pku = PrepareData(constant.VOCAB_SIZE, 'corpus/pku_training.utf8',
                              'corpus/pku_training_words.txt',
                              'corpus/pku_training_labels.txt',
                              'corpus/pku_training_dict.txt')
    prepare_pku.build_exec()
    dict_name = 'corpus/pku_training_dict.txt'
    copyfile(dict_name, 'corpus/dict.utf8')
    trans_dnn = TransformDataDNN(constant.DNN_SKIP_WINDOW, True)
    trans_dnn.generate_exe()
Exemple #3
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    def __init__(self, config, paths, vocab):
        self.vocab = vocab

        if isinstance(paths, str):
            paths = [paths]

        prepare_data = PrepareData(min_count=config.MIN_COUNT,
                                   max_length=config.MAX_LENGTH)
        parsed_pairs = sum(
            [prepare_data.read_pairs(datafile) for datafile in paths], [])

        self.data = CornellMovieDialogDataset.make_dataset(parsed_pairs, vocab)
Exemple #4
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    def parse_args(self):
        arg_parser = argparse.ArgumentParser()
        arg_parser.add_argument(
            '-n',
            '--network',
            dest='network_filename',
            type=str,
            required=True,
            help='Name of the input hdf5 file with the neural network'
        )
        arg_parser.add_argument(
            '-st',
            '--stats',
            dest='stats',
            nargs='?',
            const=True,
            required=False,
            help='Show accuracy stats',
            default=False
        )
        arg_parser.add_argument(
            '-r',
            '--print-results',
            dest='print_results',
            nargs='?',
            const=True,
            required=False,
            help='Show every board state',
            default=False
        )
        arg_parser.add_argument(
            '--disable-cuda',
            dest='disable_cuda',
            nargs='?',
            const=True,
            required=False,
            help='Add this flag to use the CPU instead of the GPU',
            default=False
        )
        arg_parser.add_argument(
            '-l',
            '--log',
            dest='log_to_file',
            nargs='?',
            const=True,
            required=False,
            default=False,
            help='Add this flag if board states should be stored in a file'
                 ' (that can be played back later with a visualizer)'
        )
        self.args = arg_parser.parse_args()

        if 'ds2048_1' in self.args.network_filename:
            self.preprocessing_method = PrepareData.pre_process1
        else:
            self.preprocessing_method = PrepareData.pre_process2
        self.input_vector_size = PrepareData.get_vector_size(self.preprocessing_method)

        self.args = arg_parser.parse_args()
        self.network_filename = self.args.network_filename
def predict_sentiment():
    input_json = request.get_json()
    input_review = json.loads(input_json["review"])
    prep = PrepareData(input_fields=config.INPUT_FIELDS,
                       text_field=config.TEXT_FIELD,
                       target_field=config.TARGET_FIELD,
                       maxlen=config.MAX_LEN,
                       padding="pre",
                       vocab_size=config.VOCAB_SIZE)
    x = prep.run_prep(input_review)
    predicted_prob = _infer(
        model_input={"inputs": {
            "text_input": x.values.tolist()
        }})["outputs"]
    predicted_prob = np.array(predicted_prob)
    sentiments = np.where(predicted_prob > 0.5, 1, 0)
    return jsonify(sentiments.tolist())
    def add_aux_corpus(self):
        src_rare_vocab = rare_vocab_create(self.src_vocab)
        trg_rare_vocab = rare_vocab_create(self.trg_vocab)
        
        #rare_vocabの単語を含む対訳を抽出
        aux_taiyaku = []
        for src in src_rare_vocab:
            aux_taiyaku.append(scraping(src, "en"))

        for trg in trg_rare_vocab:
            aux_taiyaku.append(scraping(trg, "ja"))

        aux_corpus = './../data/aux_taiyaku.tsv'
        f = open(aux_corpus, 'w')
        for s in aux_taiyaku:
            f.write(s+'\n')
        f.close()

        PrepareData.extract_each_sentence(aux_corpus, './../data/ja_aux_sentences.tsv', 'ja')
        PrepareData.extract_each_sentence(aux_corpus, './../data/en_aux_sentences.tsv', 'en')

        #aux_corpusについてもvocabを作成
        aux_src_vocab = Tokenizer.en_vocab_create('./../data/en_aux_sentences.tsv')
        aux_trg_vocab = Tokenizer.ja_vocab_create('./../data/ja_aux_sentences.tsv')

        #vocabにない、かつaux_vocabにおいてもfreq50未満の単語 が含まれている文をaux_corpusから削除
        no_use_src_vocab = rare_vocab_create(aux_src_vocab)
        no_use_trg_vocab = rare_vocab_create(aux_trg_vocab)

        for i in range(len(no_use_src_vocab)):
            if no_use_src_vocab[i] in self.src_vocab.keys():
                del no_use_src_vocab[i]

        for i in range(len(no_use_trg_vocab)):
            if no_use_trg_vocab[i] in self.trg_vocab.keys():
                del no_use_trg_vocab[i]

        no_use_vocab = no_use_src_vocab + no_use_trg_vocab
        for j in range(len(aux_taiyaku)):
            for word in no_use_vocab:
                if word in aux_taiyaku[j]:
                    del aux_taiyaku[j]
                    break

        f = open(aux_corpus, 'w')
        for s in aux_taiyaku:
            f.write(s+'\n')
        f.close()

        #トレーニングデータにaux_corpusを追加
        PrepareData.extract_each_sentence(aux_corpus, './../data/ja_sentences.tsv', 'ja')
        PrepareData.extract_each_sentence(aux_corpus, './../data/en_sentences.tsv', 'en')
Exemple #7
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    def parse_args(self):
        arg_parser = argparse.ArgumentParser()
        arg_parser.add_argument(
            '-n',
            '--network',
            dest='network_filename',
            type=str,
            required=True,
            help='Name of the input hdf5 file with the neural network')
        arg_parser.add_argument('-st',
                                '--stats',
                                dest='stats',
                                nargs='?',
                                const=True,
                                required=False,
                                help='Show accuracy stats',
                                default=False)
        arg_parser.add_argument('-r',
                                '--print-results',
                                dest='print_results',
                                nargs='?',
                                const=True,
                                required=False,
                                help='Show every board state',
                                default=False)
        arg_parser.add_argument(
            '--disable-cuda',
            dest='disable_cuda',
            nargs='?',
            const=True,
            required=False,
            help='Add this flag to use the CPU instead of the GPU',
            default=False)
        arg_parser.add_argument(
            '-l',
            '--log',
            dest='log_to_file',
            nargs='?',
            const=True,
            required=False,
            default=False,
            help='Add this flag if board states should be stored in a file'
            ' (that can be played back later with a visualizer)')
        self.args = arg_parser.parse_args()

        if 'ds2048_1' in self.args.network_filename:
            self.preprocessing_method = PrepareData.pre_process1
        else:
            self.preprocessing_method = PrepareData.pre_process2
        self.input_vector_size = PrepareData.get_vector_size(
            self.preprocessing_method)

        self.args = arg_parser.parse_args()
        self.network_filename = self.args.network_filename
Exemple #8
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def train():
	# prepare data for sentencepiece training
	PrepareData.extract_each_sentence('./../data/taiyaku.tsv', './../data/ja_sentences.tsv', 'ja')
	PrepareData.extract_each_sentence('./../data/taiyaku.tsv', './../data/en_sentences.tsv', 'en')

	# train sentencepiece model
	Tokenizer.train_sentencepiece(32000, 'ja')

	#data augment
	da = DataAugmentation()
	da.add_aux_corpus()

	# data filtering process
	fl = Filter('./../data/taiyaku.tsv')
	fl.one_multi_filter()
	print('1st done')
	fl.src_equal_trg_filter()
	print('second done')
	fl.non_alphabet_filter(0.5)
	print('')
	fl.correct_lang_filter()
	fl.update_df()

	# prepare data for feeding to a model to make
	PrepareData.prepare_tokenized_taiyaku('./../data/tokenized_taiyaku.tsv')

	t2t = PyT2T()
	# data generate
	t2t.data_gen()
	# train phase
	t2t.train()
Exemple #9
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def main():
    # 数据预处理
    data = PrepareData()
    args.src_vocab = len(data.en_word_dict)
    args.tgt_vocab = len(data.cn_word_dict)
    print("src_vocab %d" % args.src_vocab)
    print("tgt_vocab %d" % args.tgt_vocab)

    # 初始化模型
    model = make_model(
                        args.src_vocab, 
                        args.tgt_vocab, 
                        args.layers, 
                        args.d_model, 
                        args.d_ff,
                        args.h_num,
                        args.dropout
                    )

   
    if args.type == 'train':
        # 训练
        print(">>>>>>> start train")
        criterion = LabelSmoothing(args.tgt_vocab, padding_idx = 0, smoothing= 0.0)
        optimizer = NoamOpt(args.d_model, 1, 2000, torch.optim.Adam(model.parameters(), lr=0, betas=(0.9,0.98), eps=1e-9))
        
        train(data, model, criterion, optimizer)
        print("<<<<<<< finished train")
    elif args.type == "evaluate":
        # 预测
        # 先判断模型有没有训练好(前提)
        if os.path.exists(args.save_file):
            # 加载模型
            model.load_state_dict(torch.load(args.save_file))
            # 开始预测
            print(">>>>>>> start evaluate")
            evaluate(data, model)         
            print("<<<<<<< finished evaluate")
        else:
            print("Error: pleas train before evaluate")
    else:
        print("Error: please select type within [train / evaluate]")
Exemple #10
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def evaluate_model(cws, model):
    pre = PrepareData(4000,
                      'pku',
                      dict_path='corpus/pku_dict.utf8',
                      type=CorpusType.Test)
    sentences = pre.raw_lines
    labels = pre.labels_index
    corr_count = 0
    re_count = 0
    total_count = 0

    for _, (sentence, label) in enumerate(zip(sentences, labels)):
        _, tag = cws.seg(sentence, model)
        cor_count, prec_count, recall_count = estimate_cws(
            tag, np.array(label))
        corr_count += cor_count
        re_count += recall_count
        total_count += prec_count
    prec = corr_count / total_count
    recall = corr_count / re_count

    print(prec)
    print(recall)
    print(2 * prec * recall / (prec + recall))
Exemple #11
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import numpy as np
import pandas as pd
from pprint import pprint
from prepare_data import PrepareData
from sklearn.ensemble import RandomForestClassifier

prepared_data = PrepareData()

labels = prepared_data.tag
raw_data = prepared_data.raw_data
training_data = raw_data[1:]
index_data = raw_data[0]
print(np.array(labels).shape)
print(np.array(training_data).shape)

# forest = RandomForestClassifier(n_estimators=10000, random_state=0, n_jobs=-1, oob_score=True)
# forest.fit(training_data, labels)

# importances = forest.feature_importances_
# indices = np.argsort(importances)[::-1]

# print(forest.oob_score_)

# for f in range(len(index_data)):
#     print("%2d) %-*s %f" % (indices[f], 30, index_data[f], importances[indices[f]]))
import matplotlib.pyplot as plt

from sklearn import datasets, svm
from sklearn.feature_selection import SelectPercentile, f_classif, SelectKBest, chi2

###############################################################################
#!/usr/bin/env python
# coding: utf-8

from prepare_data import PrepareData
from model import LSTMClassifier
import pandas as pd
from sklearn.model_selection import train_test_split

ppd = PrepareData()
data = ppd.get_data()

lstm = LSTMClassifier()
X = lstm.get_matrix(data)
Y = pd.get_dummies(data['label']).values
X_train, X_test, Y_train, Y_test = train_test_split(X,
                                                    Y,
                                                    test_size=0.33,
                                                    random_state=42)
print(X_train.shape, Y_train.shape)
print(X_test.shape, Y_test.shape)

model = lstm.get_model(X.shape[1])
history = lstm.fit_model(model, X_train, Y_train)

validation_size = 1500
X_validate = X_test[-validation_size:]
Y_validate = Y_test[-validation_size:]
X_test = X_test[:-validation_size]
Y_test = Y_test[:-validation_size]

score, acc = model.evaluate(X_test, Y_test, verbose=2, batch_size=batch_size)
Exemple #13
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    def __init__(self, overwrite=False):
        self.overwrite = overwrite  # whether to overwrite an existing index without asking
        with open(os.path.join(self.SETTINGS_DIR, 'corpus.json'),
                  'r',
                  encoding='utf-8') as fSettings:
            self.settings = json.load(fSettings)
        self.j2h = JSON2HTML(settings=self.settings)
        self.name = self.settings['corpus_name']
        self.languages = self.settings['languages']
        if len(self.languages) <= 0:
            self.languages = [self.name]
        self.input_format = self.settings['input_format']
        self.corpus_dir = os.path.join('../corpus', self.name)
        self.iterSent = None
        if self.input_format in ['json', 'json-gzip']:
            self.iterSent = JSONDocReader(format=self.input_format,
                                          settings=self.settings)

        # Make sure only commonly used word fields and those listed
        # in corpus.json get into the words index.
        self.goodWordFields = [
            'lex',  # lemma
            'wf',  # word form (for search)
            'wf_display',  # word form (for display; optional)
            'parts',  # morpheme breaks in the word form
            'gloss',  # glosses (for display)
            'gloss_index',  # glosses (for search)
            'n_ana'  # number of analyses
        ]
        self.additionalWordFields = set()
        if 'word_fields' in self.settings:
            self.additionalWordFields |= set(self.settings['word_fields'])
        if 'word_table_fields' in self.settings:
            self.additionalWordFields |= set(
                self.settings['word_table_fields'])
        if 'accidental_word_fields' in self.settings:
            self.additionalWordFields -= set(
                self.settings['accidental_word_fields'])
        f = open(os.path.join(self.SETTINGS_DIR, 'categories.json'),
                 'r',
                 encoding='utf-8')
        categories = json.loads(f.read())
        f.close()
        self.goodWordFields += [
            'gr.' + v for lang in categories
            for v in categories[lang].values()
        ]
        self.goodWordFields = set(self.goodWordFields)
        self.characterRegexes = {}

        self.pd = PrepareData()
        self.es = Elasticsearch()
        self.es_ic = IndicesClient(self.es)
        self.shuffled_ids = [i for i in range(1, 1000000)]
        random.shuffle(self.shuffled_ids)
        self.shuffled_ids.insert(0, 0)  # id=0 is special and should not change
        self.tmpWordIDs = [{} for i in range(len(self.languages))
                           ]  # word as JSON -> its integer ID
        self.tmpLemmaIDs = [{} for i in range(len(self.languages))
                            ]  # lemma as string -> its integer ID
        # Apart from the two dictionaries above, words and lemmata
        # have string IDs starting with 'w' or 'l' followed by an integer
        self.word2lemma = [
            {} for i in range(len(self.languages))
        ]  # word/lemma ID -> ID of its lemma (or -1, if none)
        self.wordFreqs = [{} for i in range(len(self.languages))
                          ]  # word/lemma ID -> its frequency
        self.wordSFreqs = [{} for i in range(len(self.languages))
                           ]  # word/lemma ID -> its number of sentences
        self.wordDocFreqs = [
            {} for i in range(len(self.languages))
        ]  # (word/lemma ID, dID) -> word frequency in the document
        # self.wordSIDs = [{} for i in range(len(self.languages))]      # word's ID -> set of sentence IDs
        self.wordDIDs = [{} for i in range(len(self.languages))
                         ]  # word/lemma ID -> set of document IDs
        self.wfs = set()  # set of word forms (for sorting)
        self.lemmata = set()  # set of lemmata (for sorting)
        self.sID = 0  # current sentence ID for each language
        self.dID = 0  # current document ID
        self.wID = 0  # current word ID
        self.wordFreqID = 0  # current word_freq ID for word/document frequencies
        self.lemmaFreqID = 0  # current word_freq ID for lemma/document frequencies
        self.numWords = 0  # number of words in current document
        self.numSents = 0  # number of sentences in current document
        self.numWordsLang = [0] * len(
            self.languages
        )  # number of words in each language in current document
        self.numSentsLang = [0] * len(
            self.languages
        )  # number of sentences in each language in current document
        self.totalNumWords = 0
Exemple #14
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class Indexator:
    """
    Contains methods for loading the JSON documents in the corpus
    database.
    """
    SETTINGS_DIR = '../conf'
    rxBadFileName = re.compile('[^\\w_.-]*', flags=re.DOTALL)

    def __init__(self, overwrite=False):
        self.overwrite = overwrite  # whether to overwrite an existing index without asking
        with open(os.path.join(self.SETTINGS_DIR, 'corpus.json'),
                  'r',
                  encoding='utf-8') as fSettings:
            self.settings = json.load(fSettings)
        self.j2h = JSON2HTML(settings=self.settings)
        self.name = self.settings['corpus_name']
        self.languages = self.settings['languages']
        if len(self.languages) <= 0:
            self.languages = [self.name]
        self.input_format = self.settings['input_format']
        self.corpus_dir = os.path.join('../corpus', self.name)
        self.iterSent = None
        if self.input_format in ['json', 'json-gzip']:
            self.iterSent = JSONDocReader(format=self.input_format,
                                          settings=self.settings)

        # Make sure only commonly used word fields and those listed
        # in corpus.json get into the words index.
        self.goodWordFields = [
            'lex',  # lemma
            'wf',  # word form (for search)
            'wf_display',  # word form (for display; optional)
            'parts',  # morpheme breaks in the word form
            'gloss',  # glosses (for display)
            'gloss_index',  # glosses (for search)
            'n_ana'  # number of analyses
        ]
        self.additionalWordFields = set()
        if 'word_fields' in self.settings:
            self.additionalWordFields |= set(self.settings['word_fields'])
        if 'word_table_fields' in self.settings:
            self.additionalWordFields |= set(
                self.settings['word_table_fields'])
        if 'accidental_word_fields' in self.settings:
            self.additionalWordFields -= set(
                self.settings['accidental_word_fields'])
        f = open(os.path.join(self.SETTINGS_DIR, 'categories.json'),
                 'r',
                 encoding='utf-8')
        categories = json.loads(f.read())
        f.close()
        self.goodWordFields += [
            'gr.' + v for lang in categories
            for v in categories[lang].values()
        ]
        self.goodWordFields = set(self.goodWordFields)
        self.characterRegexes = {}

        self.pd = PrepareData()
        self.es = Elasticsearch()
        self.es_ic = IndicesClient(self.es)
        self.shuffled_ids = [i for i in range(1, 1000000)]
        random.shuffle(self.shuffled_ids)
        self.shuffled_ids.insert(0, 0)  # id=0 is special and should not change
        self.tmpWordIDs = [{} for i in range(len(self.languages))
                           ]  # word as JSON -> its integer ID
        self.tmpLemmaIDs = [{} for i in range(len(self.languages))
                            ]  # lemma as string -> its integer ID
        # Apart from the two dictionaries above, words and lemmata
        # have string IDs starting with 'w' or 'l' followed by an integer
        self.word2lemma = [
            {} for i in range(len(self.languages))
        ]  # word/lemma ID -> ID of its lemma (or -1, if none)
        self.wordFreqs = [{} for i in range(len(self.languages))
                          ]  # word/lemma ID -> its frequency
        self.wordSFreqs = [{} for i in range(len(self.languages))
                           ]  # word/lemma ID -> its number of sentences
        self.wordDocFreqs = [
            {} for i in range(len(self.languages))
        ]  # (word/lemma ID, dID) -> word frequency in the document
        # self.wordSIDs = [{} for i in range(len(self.languages))]      # word's ID -> set of sentence IDs
        self.wordDIDs = [{} for i in range(len(self.languages))
                         ]  # word/lemma ID -> set of document IDs
        self.wfs = set()  # set of word forms (for sorting)
        self.lemmata = set()  # set of lemmata (for sorting)
        self.sID = 0  # current sentence ID for each language
        self.dID = 0  # current document ID
        self.wID = 0  # current word ID
        self.wordFreqID = 0  # current word_freq ID for word/document frequencies
        self.lemmaFreqID = 0  # current word_freq ID for lemma/document frequencies
        self.numWords = 0  # number of words in current document
        self.numSents = 0  # number of sentences in current document
        self.numWordsLang = [0] * len(
            self.languages
        )  # number of words in each language in current document
        self.numSentsLang = [0] * len(
            self.languages
        )  # number of sentences in each language in current document
        self.totalNumWords = 0

    def delete_indices(self):
        """
        If there already exist indices with the same names,
        ask the user if they want to overwrite them. If they
        say yes, remove the indices and return True. Otherwise,
        return False.
        """
        if not self.overwrite:
            if (self.es_ic.exists(index=self.name + '.docs')
                    or self.es_ic.exists(index=self.name + '.words')
                    or self.es_ic.exists(index=self.name + '.sentences')):
                print('It seems that a corpus named "' + self.name +
                      '" already exists. ' +
                      'Do you want to overwrite it? [y/n]')
                reply = input()
                if reply.lower() != 'y':
                    print('Indexation aborted.')
                    return False
        if self.es_ic.exists(index=self.name + '.docs'):
            self.es_ic.delete(index=self.name + '.docs')
        if self.es_ic.exists(index=self.name + '.words'):
            self.es_ic.delete(index=self.name + '.words')
        if self.es_ic.exists(index=self.name + '.sentences'):
            self.es_ic.delete(index=self.name + '.sentences')
        # Obsolete index word_freq can be present in pre-2019 corpora
        if self.es_ic.exists(index=self.name + '.word_freqs'):
            self.es_ic.delete(index=self.name + '.word_freqs')
        return True

    def create_indices(self):
        """
        Create empty elasticsearch indices for corpus data, using
        mappings provided by PrepareData.
        """
        self.sentWordMapping = self.pd.generate_words_mapping(wordFreqs=False)
        self.wordMapping = self.pd.generate_words_mapping(wordFreqs=True)
        self.sentMapping = self.pd.generate_sentences_mapping(
            self.sentWordMapping)
        self.docMapping = self.pd.generate_docs_mapping()

        self.es_ic.create(index=self.name + '.docs', body=self.docMapping)
        self.es_ic.create(index=self.name + '.words', body=self.wordMapping)
        self.es_ic.create(index=self.name + '.sentences',
                          body=self.sentMapping)

    def randomize_id(self, realID):
        """
        Return a (relatively) randomized sentence ID. This randomization
        is needed in context-aware word queries where the sentences
        are iterated in the order determined by their IDs.
        """
        if realID < 0:
            return realID
        idStart, idEnd = realID // 1000000, realID % 1000000
        return idStart * 1000000 + self.shuffled_ids[idEnd]

    def enhance_word(self, word):
        """
        Add some calculated fields to the JSON word.
        """
        if 'ana' not in word:
            word['n_ana'] = 0
        else:
            word['n_ana'] = len(word['ana'])
            # n_ana is a (signed) byte, so a word can have at most 127 analyses
            if word['n_ana'] >= 127:
                word['n_ana'] = 127

    def clean_word(self, w, langID):
        """
        Clean a word object by removing unnecessary fields, lowercasing
        things if needed, etc. Return the cleaned object and the lemma.
        Add word form and lemma to the global lists.
        """
        wClean = {'lang': langID}
        lemma = ''
        for field in w:
            if field in self.goodWordFields or field in self.additionalWordFields:
                wClean[field] = w[field]
                if field == 'wf':
                    if 'wf_lowercase' not in self.settings or self.settings[
                            'wf_lowercase']:
                        wClean[field] = wClean[field].lower()
                    self.wfs.add(wClean[field])
        if 'ana' in w:
            lemma = self.get_lemma(w)
            self.lemmata.add(lemma)
            wClean['ana'] = []
            for ana in w['ana']:
                cleanAna = {}
                for anaField in ana:
                    if anaField in self.goodWordFields or anaField in self.additionalWordFields:
                        cleanAna[anaField] = ana[anaField]
                wClean['ana'].append(cleanAna)
        return wClean, lemma

    def process_sentence_words(self, words, langID):
        """
        Take words from a sentence, remove all non-searchable
        fields from them and add them to self.words dictionary.
        Add w_id and l_id properties to each word of the words list.
        Return the value of the 'sent_analyzed' meta field.
        """
        sIDAdded = set(
        )  # word IDs for which the current settence ID has been counted
        bFullyAnalyzed = True  # Whether each word in the sentence is analyzed
        bUniquelyAnalyzed = True  # Whether, in addition, each word has exactly one analysis
        for w in words:
            if w['wtype'] != 'word':
                continue
            self.numWords += 1
            self.numWordsLang[langID] += 1
            self.totalNumWords += 1
            self.enhance_word(w)

            if 'ana' not in w or len(w['ana']) <= 0:
                bFullyAnalyzed = False
                bUniquelyAnalyzed = False
            elif len(w['ana']) > 1:
                bUniquelyAnalyzed = False

            wClean, lemma = self.clean_word(w, langID)
            wCleanTxt = json.dumps(wClean, ensure_ascii=False, sort_keys=True)
            if wCleanTxt in self.tmpWordIDs[langID]:
                wID = self.tmpWordIDs[langID][wCleanTxt]
            else:
                wID = sum(
                    len(self.tmpWordIDs[i])
                    for i in range(len(self.languages)))
                self.tmpWordIDs[langID][wCleanTxt] = wID
            wID = 'w' + str(wID)
            w['w_id'] = wID
            lID = 'l0'  # Default: no analysis
            if len(lemma) > 0:
                try:
                    lID = self.tmpLemmaIDs[langID][lemma]
                except KeyError:
                    lID = sum(
                        len(self.tmpLemmaIDs[i])
                        for i in range(len(self.languages))) + 1
                    self.tmpLemmaIDs[langID][lemma] = lID
                lID = 'l' + str(lID)
                self.word2lemma[langID][wID] = lID
            w['l_id'] = lID
            for itemID in [wID, lID]:
                try:
                    self.wordFreqs[langID][itemID] += 1
                except KeyError:
                    self.wordFreqs[langID][itemID] = 1
                if itemID not in sIDAdded:
                    sIDAdded.add(itemID)
                    try:
                        self.wordSFreqs[langID][itemID] += 1
                    except KeyError:
                        self.wordSFreqs[langID][itemID] = 1
                try:
                    self.wordDIDs[langID][itemID].add(self.dID)
                except KeyError:
                    self.wordDIDs[langID][itemID] = {self.dID}
                try:
                    self.wordDocFreqs[langID][(itemID, self.dID)] += 1
                except KeyError:
                    self.wordDocFreqs[langID][(itemID, self.dID)] = 1
        if not bFullyAnalyzed:
            return 'incomplete'
        if not bUniquelyAnalyzed:
            return 'complete'
        return 'unique'

    def character_regex(self, lang):
        """
        Regex for splitting text into characters. Takes into account
        multicharacter sequences (digraphs etc.) defined in lang_props.lexicographic_order.
        """
        if lang in self.characterRegexes:
            return self.characterRegexes[lang]  # cache
        if lang not in self.settings[
                'lang_props'] or 'lexicographic_order' not in self.settings[
                    'lang_props'][lang]:
            self.characterRegexes[lang] = re.compile('.')
            return self.characterRegexes[lang]
        rxChars = '(' + '|'.join(
            re.escape(c.lower()) for c in sorted(
                self.settings['lang_props'][lang]['lexicographic_order'],
                key=lambda x: (-len(x), x)) if len(c) > 1)
        if len(rxChars) > 1:
            rxChars += '|'
        rxChars += '.)'
        rxChars = re.compile(rxChars)
        self.characterRegexes[lang] = rxChars
        return rxChars

    def make_sorting_function(self, lang):
        """
        Return a function that can be used for sorting tokens
        in a list according to the alphabetical ordering specified
        for the language lang.
        """
        sortingFunction = lambda x: x
        if lang in self.settings[
                'lang_props'] and 'lexicographic_order' in self.settings[
                    'lang_props'][lang]:
            dictSort = {
                self.settings['lang_props'][lang]['lexicographic_order'][i]:
                (i,
                 self.settings['lang_props'][lang]['lexicographic_order'][i])
                for i in range(
                    len(self.settings['lang_props'][lang]
                        ['lexicographic_order']))
            }
            maxIndex = len(dictSort)
            rxChars = self.character_regex(lang)

            def charReplaceFunction(c):
                if c in dictSort:
                    return dictSort[c]
                return (maxIndex, c)

            sortingFunction = lambda x: [
                charReplaceFunction(c) for c in rxChars.findall(x.lower())
            ]
        return sortingFunction

    def sort_words(self, lang):
        """
        Sort word forms and lemmata stored at earlier stages.
        Return dictionaries with positions of word forms and
        lemmata in the sorted list.
        If there is a custom alphabetical order for the language,
        use it. Otherwise, use standard lexicographic sorting.
        """
        wfsSorted = {}
        iOrder = 0
        sortingFunction = self.make_sorting_function(lang)
        for wf in sorted(self.wfs, key=sortingFunction):
            wfsSorted[wf] = iOrder
            iOrder += 1
        lemmataSorted = {}
        iOrder = 0
        for l in sorted(self.lemmata, key=sortingFunction):
            lemmataSorted[l] = iOrder
            iOrder += 1
        return wfsSorted, lemmataSorted

    def get_freq_ranks(self, freqsSorted):
        """
        Calculate frequency ranks and rank/quantile labels for words
        or lemmata.
        """
        freqToRank = {}
        quantiles = {}
        prevFreq = 0
        prevRank = 0
        for i in range(len(freqsSorted)):
            v = freqsSorted[i]
            if v != prevFreq:
                if prevFreq != 0:
                    freqToRank[prevFreq] = prevRank + (i - prevRank) // 2
                prevRank = i
                prevFreq = v
        if prevFreq != 0:
            freqToRank[prevFreq] = prevRank + (len(freqsSorted) -
                                               prevRank) // 2
        for q in [0.03, 0.04, 0.05, 0.1, 0.15, 0.2, 0.25, 0.5]:
            qIndex = math.ceil(q * len(freqsSorted))
            if qIndex >= len(freqsSorted):
                qIndex = len(freqsSorted) - 1
            if qIndex >= 0:
                quantiles[q] = freqsSorted[qIndex]
            else:
                quantiles[q] = 0
        return freqToRank, quantiles

    def quantile_label(self, freq, rank, quantiles):
        """
        Return a string label of the frequency rank (for frequent items)
        or quantile. This label is showed to the user in word query results.
        """
        if freq > 1 and freq >= quantiles[0.5]:
            if freq > quantiles[0.03]:
                return '#' + str(rank + 1)
            else:
                return '&gt; ' + str(
                    min(
                        math.ceil(q * 100)
                        for q in quantiles if freq >= quantiles[q])) + '%'
        return ''

    def get_lemma(self, word, lower_lemma=True):
        """
        Join all lemmata in the JSON representation of a word with
        an analysis and return them as a string.
        """
        if 'ana' not in word:
            return ''
        if 'keep_lemma_order' not in self.settings or not self.settings[
                'keep_lemma_order']:
            curLemmata = set()
            for ana in word['ana']:
                if 'lex' in ana:
                    if type(ana['lex']) == list:
                        for l in ana['lex']:
                            lAdd = l
                            if lower_lemma:
                                lAdd = lAdd.lower()
                            curLemmata.add(lAdd)
                    else:
                        lAdd = ana['lex']
                        if lower_lemma:
                            lAdd = lAdd.lower()
                        curLemmata.add(lAdd)
            return '/'.join(l for l in sorted(curLemmata))
        curLemmata = []
        for ana in word['ana']:
            if 'lex' in ana:
                if type(ana['lex']) == list:
                    for l in ana['lex']:
                        lAdd = l
                        if lower_lemma:
                            lAdd = lAdd.lower()
                        curLemmata.append(lAdd)
                else:
                    lAdd = ana['lex']
                    if lower_lemma:
                        lAdd = lAdd.lower()
                    curLemmata.append(lAdd)
        return '/'.join(curLemmata)

    def get_grdic(self, word, lang):
        """
        Join all dictionary grammar tags strings in the JSON representation of a word with
        an analysis and return them as a string.
        """
        if 'ana' not in word:
            return ''
        curGramm = set()
        translations = set()
        for ana in word['ana']:
            grTags = ''
            if 'gr.pos' in ana:
                value = ana['gr.pos']
                if type(value) == list:
                    value = ', '.join(value)
                grTags = value
            for field in sorted(ana):
                value = ana[field]
                if type(value) == list:
                    value = ', '.join(value)
                if ('lang_props' in self.settings
                        and lang in self.settings['lang_props']
                        and 'dictionary_categories'
                        in self.settings['lang_props'][lang]
                        and field.startswith('gr.')
                        and field[3:] in self.settings['lang_props'][lang]
                    ['dictionary_categories']):
                    if len(grTags) > 0:
                        grTags += ', '
                    grTags += value
                elif field.startswith('trans_'):
                    translations.add(value)
            if len(grTags) > 0:
                curGramm.add(grTags)
        return ' | '.join(grdic for grdic in sorted(curGramm)), ' | '.join(
            tr for tr in sorted(translations))

    def iterate_lemmata(self, langID, lemmataSorted):
        """
        Iterate over all lemmata for one language collected at the
        word iteration stage.
        """
        lFreqsSorted = [
            self.wordFreqs[langID][itemID] for itemID in self.wordFreqs[langID]
            if itemID.startswith('l')
        ]
        lFreqsSorted.sort(reverse=True)
        lemmaFreqToRank, quantiles = self.get_freq_ranks(lFreqsSorted)
        iLemma = 0
        for l, lID in self.tmpLemmaIDs[langID].items():
            lID = 'l' + str(lID)
            if iLemma % 250 == 0:
                print('indexing lemma', iLemma)
            lOrder = lemmataSorted[l]
            lemmaJson = {
                'wf':
                l,
                'wtype':
                'lemma',
                'lang':
                langID,
                'l_order':
                lOrder,
                'freq':
                self.wordFreqs[langID][lID],
                'lemma_freq':
                self.wordFreqs[langID][lID],
                'rank_true':
                lemmaFreqToRank[self.wordFreqs[langID][lID]],
                'rank':
                self.quantile_label(
                    self.wordFreqs[langID][lID],
                    lemmaFreqToRank[self.wordFreqs[langID][lID]], quantiles),
                'n_sents':
                self.wordSFreqs[langID][lID],
                'n_docs':
                len(self.wordDIDs[langID][lID]),
                'freq_join':
                'word'
            }
            curAction = {
                '_index': self.name + '.words',
                '_id': lID,
                '_source': lemmaJson
            }
            iLemma += 1
            yield curAction

            for docID in self.wordDIDs[langID][lID]:
                lfreqJson = {
                    'wtype': 'word_freq',
                    'l_id': lID,
                    'd_id': docID,
                    'l_order': lOrder,
                    'freq': self.wordDocFreqs[langID][(lID, docID)],
                    'freq_join': {
                        'name': 'word_freq',
                        'parent': lID
                    }
                }
                curAction = {
                    '_index': self.name + '.words',
                    '_id': 'lfreq' + str(self.lemmaFreqID),
                    '_source': lfreqJson,
                    '_routing': lID
                }
                self.lemmaFreqID += 1
                yield curAction

    def iterate_words(self):
        """
        Iterate through all words collected at the previous
        stage. Return JSON objects with actions for bulk indexing
        in Elasticsearch.
        """
        self.wID = 0

        for langID in range(len(self.languages)):
            wfsSorted, lemmataSorted = self.sort_words(self.languages[langID])
            iWord = 0
            print('Processing words in ' + self.languages[langID] + '...')

            wFreqsSorted = [
                self.wordFreqs[langID][itemID]
                for itemID in self.wordFreqs[langID] if itemID.startswith('w')
            ]
            wFreqsSorted.sort(reverse=True)
            wordFreqToRank, quantiles = self.get_freq_ranks(wFreqsSorted)

            lFreqsSorted = [
                self.wordFreqs[langID][itemID]
                for itemID in self.wordFreqs[langID] if itemID.startswith('l')
            ]
            lFreqsSorted.sort(reverse=True)
            lemmaFreqToRank, lemmaQuantiles = self.get_freq_ranks(lFreqsSorted)

            # for wID in self.wordFreqs[langID]:
            for w, wID in self.tmpWordIDs[langID].items():
                wID = 'w' + str(wID)
                if iWord % 500 == 0:
                    print('indexing word', iWord)
                try:
                    lID = self.word2lemma[langID][wID]
                except KeyError:
                    lID = 'l0'
                wJson = json.loads(w)
                wfOrder = len(wfsSorted) + 1
                if 'wf' in wJson:
                    wfOrder = wfsSorted[wJson['wf']]
                lOrder = len(lemmataSorted) + 1
                if 'ana' in wJson:
                    lOrder = lemmataSorted[self.get_lemma(wJson)]
                wJson['wf_order'] = wfOrder
                wJson['l_order'] = lOrder
                wJson['l_id'] = lID
                wordFreq = self.wordFreqs[langID][wID]
                lemmaFreq = self.wordFreqs[langID][lID]
                wJson['freq'] = wordFreq
                wJson['lemma_freq'] = lemmaFreq
                # wJson['sids'] = [sid for sid in sorted(self.wordSIDs[langID][wID])]
                wJson['dids'] = [
                    did for did in sorted(self.wordDIDs[langID][wID])
                ]
                wJson['n_sents'] = self.wordSFreqs[langID][wID]
                wJson['n_docs'] = len(wJson['dids'])
                wJson['rank_true'] = wordFreqToRank[
                    wJson['freq']]  # for the calculations
                wJson['lemma_rank_true'] = lemmaFreqToRank[
                    self.wordFreqs[langID][lID]]  # for the calculations
                wJson['rank'] = self.quantile_label(wJson['freq'],
                                                    wJson['rank_true'],
                                                    quantiles)  # for the user
                wJson['freq_join'] = 'word'
                wJson['wtype'] = 'word'
                curAction = {
                    '_index': self.name + '.words',
                    '_id': wID,
                    '_source': wJson
                }
                yield curAction

                for docID in wJson['dids']:
                    wfreqJson = {
                        'wtype': 'word_freq',
                        'w_id': wID,
                        'l_id': lID,
                        'd_id': docID,
                        'wf_order': wfOrder,
                        'l_order': lOrder,
                        'freq': self.wordDocFreqs[langID][(wID, docID)],
                        'freq_join': {
                            'name': 'word_freq',
                            'parent': wID
                        }
                    }
                    curAction = {
                        '_index': self.name + '.words',
                        '_id': 'wfreq' + str(self.wordFreqID),
                        '_source': wfreqJson,
                        '_routing': wID
                    }
                    self.wordFreqID += 1
                    yield curAction
                iWord += 1
                self.wID += 1
            for lAction in self.iterate_lemmata(langID, lemmataSorted):
                yield lAction
        emptyLemmaJson = {
            'wf': '',
            'wtype': 'lemma',
            'freq': 0,
            'rank_true': -1
        }
        curAction = {
            '_index': self.name + '.words',
            '_id': 'l0',  # l prefix stands for "lemma"
            '_source': emptyLemmaJson
        }
        yield curAction
        self.wfs = None
        self.lemmata = None

    def generate_dictionary(self):
        """
        For each language, print out an HTML dictionary containing all lexemes of the corpus.
        """
        for langID in range(len(self.languages)):
            iWord = 0
            print('Generating dictionary for ' + self.languages[langID] +
                  '...')
            lexFreqs = {}  # lemma ID -> its frequency
            wFreqsSorted = [
                v
                for v in sorted(self.wordFreqs[langID].values(), reverse=True)
            ]
            freqToRank, quantiles = self.get_freq_ranks(wFreqsSorted)
            # for wID in self.wordFreqs[langID]:
            for w, wID in self.tmpWordIDs[langID].items():
                wID = 'w' + str(wID)
                if iWord % 1000 == 0:
                    print('processing word', iWord, 'for the dictionary')
                iWord += 1
                wJson = json.loads(w)
                if 'ana' not in wJson or len(wJson['ana']) <= 0:
                    continue
                lemma = self.get_lemma(wJson, lower_lemma=False)
                grdic, translations = self.get_grdic(wJson,
                                                     self.languages[langID])
                wordFreq = self.wordFreqs[langID][wID]
                lexTuple = (lemma, grdic, translations)
                if lexTuple not in lexFreqs:
                    lexFreqs[lexTuple] = wordFreq
                else:
                    lexFreqs[lexTuple] += wordFreq
            if len(lexFreqs) <= 0:
                continue

            if not os.path.exists('../search/web_app/templates/dictionaries'):
                os.makedirs('../search/web_app/templates/dictionaries')
            fOut = open(os.path.join(
                '../search/web_app/templates/dictionaries',
                'dictionary_' + self.settings['corpus_name'] + '_' +
                self.languages[langID] + '.html'),
                        'w',
                        encoding='utf-8')
            fOut.write(
                '<h1 class="dictionary_header"> {{ _(\'Dictionary_header\') }} '
                '({{ _(\'langname_' + self.languages[langID] +
                '\') }})</h1>\n')
            prevLetter = ''
            sortingFunction = self.make_sorting_function(
                self.settings['languages'][langID])
            for lemma, grdic, trans in sorted(
                    lexFreqs,
                    key=lambda x:
                (sortingFunction(x[0].lower()), -lexFreqs[x])):
                if len(lemma) <= 0:
                    continue
                mChar = self.character_regex(self.languages[langID]).search(
                    lemma.lower())
                if mChar is None:
                    curLetter = '*'
                else:
                    curLetter = mChar.group(0)
                if curLetter != prevLetter:
                    if prevLetter != '':
                        fOut.write('</tbody>\n</table>\n')
                    fOut.write('<h2 class="dictionary_letter">' +
                               curLetter.upper() + '</h2>\n')
                    fOut.write('<table class="dictionary_table">\n<thead>\n'
                               '<th>{{ _(\'word_th_lemma\') }}</th>'
                               '<th>{{ _(\'word_th_gr\') }}</th>'
                               '<th>{{ _(\'word_th_trans_en\') }}</th>'
                               '<th>{{ _(\'word_th_frequency\') }}</th>'
                               '</thead>\n<tbody>\n')
                    prevLetter = curLetter
                fOut.write('<tr>\n<td class="dictionary_lemma">' + lemma +
                           '</td><td>' + grdic + '</td>'
                           '<td>' + trans + '</td><td>' +
                           str(lexFreqs[(lemma, grdic, trans)]) +
                           '</td></tr>\n')
            if prevLetter != '':
                fOut.write('</tbody>\n</table>\n')
            fOut.close()

    def index_words(self):
        """
        Index all words that have been collected at the previous stage
        in self.words (while the sentences were being indexed).
        """
        bulk(self.es, self.iterate_words(), chunk_size=300, request_timeout=60)
        if 'generate_dictionary' in self.settings and self.settings[
                'generate_dictionary']:
            self.generate_dictionary()

    def add_parallel_sids(self, sentences, paraIDs):
        """
        In the parallel corpus, add the IDs of aligned sentences in other languages
        to each sentence that has a para_id.
        """
        for s in sentences:
            if 'para_alignment' not in s['_source'] or 'lang' not in s[
                    '_source']:
                continue
            langID = s['_source']['lang']
            for pa in s['_source']['para_alignment']:
                paraID = pa['para_id']
                pa['sent_ids'] = []
                for i in range(len(self.languages)):
                    if i == langID:
                        continue
                    if paraID in paraIDs[i]:
                        pa['sent_ids'] += paraIDs[i][paraID]

    def iterate_sentences(self, fname):
        self.numSents = 0
        prevLast = False
        sentences = []
        paraIDs = [{} for i in range(len(self.languages))]
        for s, bLast in self.iterSent.get_sentences(fname):
            if 'lang' in s:
                langID = s['lang']
            else:
                langID = 0
                s['lang'] = langID
            s['n_words'] = 0
            if 'words' in s:
                sentAnaMeta = self.process_sentence_words(s['words'], langID)
                s['n_words'] = sum(1 for w in s['words']
                                   if 'wtype' in w and w['wtype'] == 'word')
                if 'meta' not in s:
                    s['meta'] = {}
                s['meta']['sent_analyses'] = sentAnaMeta
            if prevLast:
                prevLast = False
            elif self.numSents > 0:
                s['prev_id'] = self.randomize_id(self.sID - 1)
            if not bLast and 'last' not in s:
                s['next_id'] = self.randomize_id(self.sID + 1)
            else:
                prevLast = True
            s['doc_id'] = self.dID
            if 'meta' in s:
                for metaField in [
                        mf for mf in s['meta'].keys()
                        if not (mf.startswith('year') or mf.endswith('_kw'))
                ]:
                    s['meta'][metaField + '_kw'] = s['meta'][metaField]
            # self.es.index(index=self.name + '.sentences',
            #               id=self.sID,
            #               body=s)
            curAction = {
                '_index': self.name + '.sentences',
                '_id': self.randomize_id(self.sID),
                '_source': s
            }
            if len(self.languages) <= 1:
                yield curAction
            else:
                sentences.append(curAction)
                if 'para_alignment' in s:
                    s['para_ids'] = []
                    for pa in s['para_alignment']:
                        paraID = str(self.dID) + '_' + str(pa['para_id'])
                        pa['para_id'] = paraID
                        s['para_ids'].append(paraID)
                        try:
                            paraIDs[langID][paraID].append(
                                self.randomize_id(self.sID))
                        except KeyError:
                            paraIDs[langID][paraID] = [
                                self.randomize_id(self.sID)
                            ]
            if self.sID % 500 == 0:
                print('Indexing sentence', self.sID, ',', self.totalNumWords,
                      'words so far.')
            self.numSents += 1
            self.numSentsLang[langID] += 1
            self.sID += 1
        if len(self.languages) > 1:
            self.add_parallel_sids(sentences, paraIDs)
            for s in sentences:
                yield s

    @staticmethod
    def add_meta_keywords(meta):
        """
        For each text field in the metadata, add a keyword version
        of the same field.
        """
        for field in [k for k in meta.keys() if not k.startswith('year')]:
            meta[field + '_kw'] = meta[field]

    def index_doc(self, fname):
        """
        Store the metadata of the source file.
        """
        if self.dID % 100 == 0:
            print('Indexing document', self.dID)
        meta = self.iterSent.get_metadata(fname)
        self.add_meta_keywords(meta)
        meta['n_words'] = self.numWords
        meta['n_sents'] = self.numSents
        if len(self.settings['languages']) > 1:
            for i in range(len(self.languages)):
                meta['n_words_' + self.languages[i]] = self.numWordsLang[i]
                meta['n_sents_' + self.languages[i]] = self.numSentsLang[i]
        self.numWords = 0
        self.numSents = 0
        self.numWordsLang = [0] * len(self.languages)
        self.numSentsLang = [0] * len(self.languages)
        try:
            self.es.index(index=self.name + '.docs', id=self.dID, body=meta)
        except RequestError as err:
            print('Metadata error: {0}'.format(err))
            shortMeta = {}
            if 'filename' in meta:
                shortMeta['filename'] = meta['filename']
            if 'title' in meta:
                shortMeta['title'] = meta['title']
                shortMeta['title_kw'] = meta['title']
                self.es.index(index=self.name + '.docs',
                              id=self.dID,
                              body=shortMeta)
        if ('fulltext_view_enabled' in self.settings
                and self.settings['fulltext_view_enabled']
                and 'fulltext_id' in meta):
            fnameOut = meta['fulltext_id'] + '.json'
            self.j2h.process_file(
                fname,
                os.path.join('../search/corpus_html', self.name, fnameOut))
        self.dID += 1

    def index_dir(self):
        """
        Index all files from the corpus directory, sorted by their size
        in decreasing order. Such sorting helps prevent memory errors
        when indexing large corpora, as the default behavior is to load
        the whole file is into memory, and there is more free memory
        in the beginning of the process. If MemoryError occurs, the
        iterative JSON parser is used, which works much slower.
        """
        filenames = []
        for root, dirs, files in os.walk(self.corpus_dir):
            for fname in files:
                if (not ((self.settings['input_format'] == 'json'
                          and fname.lower().endswith('.json')) or
                         (self.settings['input_format'] == 'json-gzip'
                          and fname.lower().endswith('.json.gz')))):
                    continue
                fnameFull = os.path.join(root, fname)
                filenames.append((fnameFull, os.path.getsize(fnameFull)))
        if len(filenames) <= 0:
            print('There are no files in this corpus.')
            return
        for fname, fsize in sorted(filenames, key=lambda p: -p[1]):
            # print(fname, fsize)
            if 'sample_size' in self.settings and 0 < self.settings[
                    'sample_size'] < 1:
                # Only take a random sample of the source files (for test purposes)
                if random.random() > self.settings['sample_size']:
                    continue
            bulk(self.es,
                 self.iterate_sentences(fname),
                 chunk_size=200,
                 request_timeout=60)
            self.index_doc(fname)
        self.index_words()

    def compile_translations(self):
        """
        Compile flask_babel translations in ../search/web_app.
        """
        pythonPath = ''
        for p in sys.path:
            if re.search('Python3[^/\\\\]*[/\\\\]?$', p) is not None:
                pythonPath = p
                break
        if len(pythonPath) <= 0:
            pyBabelPath = 'pybabel'
        else:
            pyBabelPath = os.path.join(pythonPath, 'Scripts', 'pybabel')
        try:
            subprocess.run(
                [pyBabelPath, 'compile', '-d', 'translations_pybabel'],
                cwd='../search/web_app',
                check=True)
        except:
            print('Could not compile translations with ' + pyBabelPath + ' .')
        else:
            print('Interface translations compiled.')

    def load_corpus(self):
        """
        Drop the current database, if any, and load the entire corpus.
        """
        t1 = time.time()
        # self.compile_translations()
        indicesDeleted = self.delete_indices()
        if not indicesDeleted:
            return
        self.create_indices()
        self.index_dir()
        t2 = time.time()
        print('Corpus indexed in', t2 - t1, 'seconds:', self.dID, 'documents,',
              self.sID, 'sentences,', self.totalNumWords, 'words,',
              sum(len(self.wordFreqs[i]) for i in range(len(self.languages))),
              'word types (different words).')
Exemple #15
0
class Indexator:
    """
    Contains methods for loading the JSON documents in the corpus
    database.
    """
    SETTINGS_DIR = '../conf'

    def __init__(self):
        f = open(os.path.join(self.SETTINGS_DIR, 'corpus.json'),
                 'r',
                 encoding='utf-8')
        self.settings = json.loads(f.read())
        f.close()
        self.name = self.settings['corpus_name']
        self.languages = self.settings['languages']
        if len(self.languages) <= 0:
            self.languages = [self.name]
        self.input_format = self.settings['input_format']
        self.corpus_dir = os.path.join('../corpus', self.name)
        self.iterSent = None
        if self.input_format in ['json', 'json-gzip']:
            self.iterSent = JSONDocReader(format=self.input_format)
        self.goodWordFields = [
            'lex', 'wf', 'wf_display', 'parts', 'gloss', 'gloss_index',
            'n_ana', 'trans_en', 'trans_ru'
        ]
        self.AdditionalWordFields = set()
        if 'word_fields' in self.settings:
            self.AdditionalWordFields |= set(self.settings['word_fields'])
        if 'word_table_fields' in self.settings:
            self.AdditionalWordFields |= set(
                self.settings['word_table_fields'])
        f = open(os.path.join(self.SETTINGS_DIR, 'categories.json'),
                 'r',
                 encoding='utf-8')
        categories = json.loads(f.read())
        self.goodWordFields += [
            'gr.' + v for lang in categories
            for v in categories[lang].values()
        ]
        self.goodWordFields = set(self.goodWordFields)
        f.close()
        self.pd = PrepareData()
        self.es = Elasticsearch()
        self.es_ic = IndicesClient(self.es)
        self.shuffled_ids = [i for i in range(1, 1000000)]
        random.shuffle(self.shuffled_ids)
        self.shuffled_ids.insert(0, 0)  # id=0 is special and should not change
        self.tmpWordIDs = [{} for i in range(len(self.languages))
                           ]  # word as JSON -> its integer ID
        self.tmpLemmaIDs = [{} for i in range(len(self.languages))
                            ]  # lemma as string -> its integer ID
        self.word2lemma = [{} for i in range(len(self.languages))
                           ]  # word's ID -> ID of its lemma (or -1, if none)
        self.wordFreqs = [{} for i in range(len(self.languages))
                          ]  # word's ID -> its frequency
        self.wordSFreqs = [{} for i in range(len(self.languages))
                           ]  # word's ID -> its number of sentences
        self.wordDocFreqs = [
            {} for i in range(len(self.languages))
        ]  # (word's ID, dID) -> word frequency in the document
        # self.wordSIDs = [{} for i in range(len(self.languages))]      # word's ID -> set of sentence IDs
        self.wordDIDs = [{} for i in range(len(self.languages))
                         ]  # word's ID -> set of document IDs
        self.wfs = set()  # set of word forms (for sorting)
        self.lemmata = set()  # set of lemmata (for sorting)
        self.sID = 0  # current sentence ID for each language
        self.dID = 0  # current document ID
        self.wID = 0  # current word ID
        self.wordFreqID = 0
        self.numWords = 0  # number of words in current document
        self.numSents = 0  # number of sentences in current document
        self.numWordsLang = [0] * len(
            self.languages
        )  # number of words in each language in current document
        self.numSentsLang = [0] * len(
            self.languages
        )  # number of sentences in each language in current document
        self.totalNumWords = 0

    def delete_indices(self):
        if self.es_ic.exists(index=self.name + '.docs'):
            self.es_ic.delete(index=self.name + '.docs')
        if self.es_ic.exists(index=self.name + '.words'):
            self.es_ic.delete(index=self.name + '.words')
        if self.es_ic.exists(index=self.name + '.word_freqs'):
            self.es_ic.delete(index=self.name + '.word_freqs')
        if self.es_ic.exists(index=self.name + '.sentences'):
            self.es_ic.delete(index=self.name + '.sentences')

    def create_indices(self):
        self.wordMapping = self.pd.generate_words_mapping()
        self.wordFreqMapping = self.pd.generate_wordfreq_mapping()
        self.sentMapping = self.pd.generate_sentences_mapping(self.wordMapping)
        self.docMapping = self.pd.generate_docs_mapping()
        self.es_ic.create(index=self.name + '.docs', body=self.docMapping)
        self.es_ic.create(index=self.name + '.words', body=self.wordMapping)
        self.es_ic.create(index=self.name + '.sentences',
                          body=self.sentMapping)

    def randomize_id(self, realID):
        """
        Return a (relatively) randomized sentence ID. This randomization
        is needed in context-aware word queries where the sentences
        are iterated in the order determined by their IDs.
        """
        if realID < 0:
            return realID
        idStart, idEnd = realID // 1000000, realID % 1000000
        return idStart * 1000000 + self.shuffled_ids[idEnd]

    def enhance_word(self, word):
        """
        Add some calculated fields to the JSON word.
        """
        if 'ana' not in word:
            word['n_ana'] = 0
        else:
            word['n_ana'] = len(word['ana'])
            if word['n_ana'] >= 127:
                word['n_ana'] = 127

    def process_sentence_words(self, words, langID):
        """
        Take words list from a sentence, remove all non-searchable
        fields from them and add them to self.words dictionary.
        Add w_id property to each word of the words list.
        """
        sIDAdded = set(
        )  # word IDs for which the current settence ID has been counted for it
        for w in words:
            if w['wtype'] != 'word':
                continue
            self.numWords += 1
            self.numWordsLang[langID] += 1
            self.totalNumWords += 1
            self.enhance_word(w)
            wClean = {'lang': langID}
            lemma = ''
            for field in w:
                if field in self.goodWordFields or field in self.AdditionalWordFields:
                    wClean[field] = w[field]
                    if field == 'wf':
                        if 'wf_lowercase' not in self.settings or self.settings[
                                'wf_lowercase']:
                            wClean[field] = wClean[field].lower()
                        self.wfs.add(wClean[field])
            if 'ana' in w:
                lemma = self.get_lemma(w)
                self.lemmata.add(lemma)
                wClean['ana'] = []
                for ana in w['ana']:
                    cleanAna = {}
                    for anaField in ana:
                        if anaField in self.goodWordFields or anaField in self.AdditionalWordFields:
                            cleanAna[anaField] = ana[anaField]
                    wClean['ana'].append(cleanAna)
            wCleanTxt = json.dumps(wClean, ensure_ascii=False, sort_keys=True)
            if wCleanTxt in self.tmpWordIDs[langID]:
                wID = self.tmpWordIDs[langID][wCleanTxt]
            else:
                wID = sum(
                    len(self.tmpWordIDs[i])
                    for i in range(len(self.languages)))
                self.tmpWordIDs[langID][wCleanTxt] = wID
            w['w_id'] = wID
            if len(lemma) > 0:
                try:
                    lemmaID = self.tmpLemmaIDs[langID][lemma]
                except KeyError:
                    lemmaID = sum(
                        len(self.tmpLemmaIDs[i])
                        for i in range(len(self.languages))) + 1
                    self.tmpLemmaIDs[langID][lemma] = lemmaID
                self.word2lemma[langID][wID] = lemmaID

            try:
                self.wordFreqs[langID][wID] += 1
            except KeyError:
                self.wordFreqs[langID][wID] = 1
            if wID not in sIDAdded:
                sIDAdded.add(wID)
                try:
                    self.wordSFreqs[langID][wID] += 1
                except KeyError:
                    self.wordSFreqs[langID][wID] = 1
            try:
                self.wordDIDs[langID][wID].add(self.dID)
            except KeyError:
                self.wordDIDs[langID][wID] = {self.dID}
            try:
                self.wordDocFreqs[langID][(wID, self.dID)] += 1
            except KeyError:
                self.wordDocFreqs[langID][(wID, self.dID)] = 1

    def sort_words(self):
        """
        Sort word forms and lemmata stored at earlier stages.
        Return dictionaries with positions of word forms and
        lemmata in the sorted list. Delete the original lists.
        """
        wfsSorted = {}
        iOrder = 0
        for wf in sorted(self.wfs):
            wfsSorted[wf] = iOrder
            iOrder += 1
        self.wfs = None
        lemmataSorted = {}
        iOrder = 0
        for l in sorted(self.lemmata):
            lemmataSorted[l] = iOrder
            iOrder += 1
        self.lemmata = None
        return wfsSorted, lemmataSorted

    def get_freq_ranks(self, freqsSorted):
        """
        Calculate frequency ranks and rank/quantile labels for words
        or lemmata.
        """
        freqToRank = {}
        quantiles = {}
        prevFreq = 0
        prevRank = 0
        for i in range(len(freqsSorted)):
            v = freqsSorted[i]
            if v != prevFreq:
                if prevFreq != 0:
                    freqToRank[prevFreq] = prevRank + (i - prevRank) // 2
                prevRank = i
                prevFreq = v
        if prevFreq != 0:
            freqToRank[prevFreq] = prevRank + (len(freqsSorted) -
                                               prevRank) // 2
        for q in [0.03, 0.04, 0.05, 0.1, 0.15, 0.2, 0.25, 0.5]:
            qIndex = math.ceil(q * len(freqsSorted))
            if qIndex >= len(freqsSorted):
                qIndex = len(freqsSorted) - 1
            if qIndex >= 0:
                quantiles[q] = freqsSorted[qIndex]
            else:
                quantiles[q] = 0
        return freqToRank, quantiles

    def quantile_label(self, freq, rank, quantiles):
        """
        Return a string label of the frequency rank (for frequent items)
        or quantile. This label is showed to the user in word query results.
        """
        if freq > 1 and freq >= quantiles[0.5]:
            if freq > quantiles[0.03]:
                return '#' + str(rank + 1)
            else:
                return '&gt; ' + str(
                    min(
                        math.ceil(q * 100)
                        for q in quantiles if freq >= quantiles[q])) + '%'
        return ''

    def get_lemma(self, word):
        """
        Join all lemmata in the JSON representation of a word with
        an analysis and return them as a string.
        """
        if 'ana' not in word:
            return ''
        if 'keep_lemma_order' not in self.settings or not self.settings[
                'keep_lemma_order']:
            curLemmata = set()
            for ana in word['ana']:
                if 'lex' in ana:
                    if type(ana['lex']) == list:
                        for l in ana['lex']:
                            curLemmata.add(l.lower())
                    else:
                        curLemmata.add(ana['lex'].lower())
            return '/'.join(l for l in sorted(curLemmata))
        curLemmata = []
        for ana in word['ana']:
            if 'lex' in ana:
                if type(ana['lex']) == list:
                    for l in ana['lex']:
                        curLemmata.append(l.lower())
                else:
                    curLemmata.append(ana['lex'].lower())
        return '/'.join(curLemmata)

    def iterate_lemmata(self, langID, lemmaFreqs, lemmaDIDs):
        """
        Iterate over all lemmata for one language collected at the
        word iteration stage.
        """
        lFreqsSorted = [v for v in sorted(lemmaFreqs.values(), reverse=True)]
        freqToRank, quantiles = self.get_freq_ranks(lFreqsSorted)
        iLemma = 0
        for l, lID in self.tmpLemmaIDs[langID].items():
            #if iLemma % 250 == 0:
            #   print('indexing lemma', iLemma)
            lemmaJson = {
                'wf':
                l,
                'freq':
                lemmaFreqs[lID],
                'rank_true':
                freqToRank[lemmaFreqs[lID]],
                'rank':
                self.quantile_label(lemmaFreqs[lID],
                                    freqToRank[lemmaFreqs[lID]], quantiles),
                'n_docs':
                len(lemmaDIDs[lID])
            }
            curAction = {
                '_index': self.name + '.words',
                '_type': 'lemma',
                '_id': lID,
                '_source': lemmaJson
            }
            iLemma += 1
            yield curAction

    def iterate_words(self):
        """
        Iterate through all words collected at the previous
        stage. Return JSON objects with actions for bulk indexing
        in Elasticsearch.
        """
        self.wID = 0
        wfsSorted, lemmataSorted = self.sort_words()

        for langID in range(len(self.languages)):
            iWord = 0
            #print('Processing words in ' + self.languages[langID] + '...')
            lemmaFreqs = {}  # lemma ID -> its frequency
            lemmaDIDs = {}  # lemma ID -> its document IDs
            wFreqsSorted = [
                v
                for v in sorted(self.wordFreqs[langID].values(), reverse=True)
            ]
            freqToRank, quantiles = self.get_freq_ranks(wFreqsSorted)
            # for wID in self.wordFreqs[langID]:
            for w, wID in self.tmpWordIDs[langID].items():
                #if iWord % 500 == 0:
                # print('indexing word', iWord)
                try:
                    lID = self.word2lemma[langID][wID]
                except KeyError:
                    lID = 0
                wJson = json.loads(w)
                wfOrder = len(wfsSorted) + 1
                if 'wf' in wJson:
                    wfOrder = wfsSorted[wJson['wf']]
                lOrder = len(lemmataSorted) + 1
                if 'ana' in wJson:
                    lOrder = lemmataSorted[self.get_lemma(wJson)]
                wJson['wf_order'] = wfOrder
                wJson['l_order'] = lOrder
                wordFreq = self.wordFreqs[langID][wID]
                wJson['freq'] = wordFreq
                try:
                    lemmaFreqs[lID] += wordFreq
                except KeyError:
                    lemmaFreqs[lID] = wordFreq
                if lID != 0:
                    try:
                        lemmaDIDs[lID] |= self.wordDIDs[langID][wID]
                    except KeyError:
                        lemmaDIDs[lID] = set(self.wordDIDs[langID][wID])
                # wJson['sids'] = [sid for sid in sorted(self.wordSIDs[langID][wID])]
                wJson['dids'] = [
                    did for did in sorted(self.wordDIDs[langID][wID])
                ]
                wJson['n_sents'] = self.wordSFreqs[langID][wID]
                wJson['n_docs'] = len(wJson['dids'])
                wJson['rank_true'] = freqToRank[
                    wJson['freq']]  # for the calculations
                wJson['rank'] = self.quantile_label(wJson['freq'],
                                                    wJson['rank_true'],
                                                    quantiles)  # for the user
                curAction = {
                    '_index': self.name + '.words',
                    '_type': 'word',
                    '_id': wID,
                    '_source': wJson,
                    '_parent': lID
                }
                yield curAction

                for docID in wJson['dids']:
                    wfreqJson = {
                        'w_id': wID,
                        'd_id': docID,
                        'wf_order': wfOrder,
                        'l_order': lOrder,
                        'freq': self.wordDocFreqs[langID][(wID, docID)]
                    }
                    curAction = {
                        '_index': self.name + '.words',
                        '_type': 'word_freq',
                        '_id': self.wordFreqID,
                        '_source': wfreqJson,
                        '_parent': wID,
                        '_routing': lID
                    }
                    self.wordFreqID += 1
                    yield curAction
                iWord += 1
                self.wID += 1
            for lAction in self.iterate_lemmata(langID, lemmaFreqs, lemmaDIDs):
                yield lAction
        emptyLemmaJson = {'wf': 0, 'freq': 0, 'rank_true': -1}
        curAction = {
            '_index': self.name + '.words',
            '_type': 'lemma',
            '_id': 0,
            '_source': emptyLemmaJson
        }
        yield curAction

    def index_words(self):
        """
        Index all words that have been collected at the previous stage
        in self.words (while the sentences were being indexed).
        """
        bulk(self.es, self.iterate_words(), chunk_size=300, request_timeout=60)

    def add_parallel_sids(self, sentences, paraIDs):
        """
        In the parallel corpus, add the IDs of aligned sentences in other languages
        to each sentence that has a para_id.
        """
        for s in sentences:
            if 'para_alignment' not in s['_source'] or 'lang' not in s[
                    '_source']:
                continue
            langID = s['_source']['lang']
            for pa in s['_source']['para_alignment']:
                paraID = pa['para_id']
                pa['sent_ids'] = []
                for i in range(len(self.languages)):
                    if i == langID:
                        continue
                    if paraID in paraIDs[i]:
                        pa['sent_ids'] += paraIDs[i][paraID]

    def iterate_sentences(self, fname):
        self.numSents = 0
        prevLast = False
        sentences = []
        paraIDs = [{} for i in range(len(self.languages))]
        for s, bLast in self.iterSent.get_sentences(fname):
            if 'lang' in s:
                langID = s['lang']
            else:
                langID = 0
                s['lang'] = langID
            s['n_words'] = 0
            if 'words' in s:
                self.process_sentence_words(s['words'], langID)
                s['n_words'] = sum(1 for w in s['words']
                                   if 'wtype' in w and w['wtype'] == 'word')
            if prevLast:
                prevLast = False
            elif self.numSents > 0:
                s['prev_id'] = self.randomize_id(self.sID - 1)
            if not bLast and 'last' not in s:
                s['next_id'] = self.randomize_id(self.sID + 1)
            else:
                prevLast = True
            s['doc_id'] = self.dID
            if 'meta' in s:
                for metaField in [
                        mf for mf in s['meta'].keys()
                        if not mf.startswith('year')
                ]:
                    s['meta'][metaField + '_kw'] = s['meta'][metaField]
            # self.es.index(index=self.name + '.sentences',
            #               doc_type='sentence',
            #               id=self.sID,
            #               body=s)
            curAction = {
                '_index': self.name + '.sentences',
                '_type': 'sentence',
                '_id': self.randomize_id(self.sID),
                '_source': s
            }
            if len(self.languages) <= 1:
                yield curAction
            else:
                sentences.append(curAction)
                if 'para_alignment' in s:
                    s['para_ids'] = []
                    for pa in s['para_alignment']:
                        paraID = str(self.dID) + '_' + str(pa['para_id'])
                        pa['para_id'] = paraID
                        s['para_ids'].append(paraID)
                        try:
                            paraIDs[langID][paraID].append(
                                self.randomize_id(self.sID))
                        except KeyError:
                            paraIDs[langID][paraID] = [
                                self.randomize_id(self.sID)
                            ]
            #if self.sID % 500 == 0:
            #   print('Indexing sentence', self.sID, ',', self.totalNumWords, 'words so far.')
            self.numSents += 1
            self.numSentsLang[langID] += 1
            self.sID += 1
        if len(self.languages) > 1:
            self.add_parallel_sids(sentences, paraIDs)
            for s in sentences:
                yield s

    @staticmethod
    def add_meta_keywords(meta):
        """
        For each text field in the metadata, add a keyword version
        of the same field.
        """
        for field in [k for k in meta.keys() if not k.startswith('year')]:
            meta[field + '_kw'] = meta[field]

    def index_doc(self, fname):
        """
        Store the metadata of the source file.
        """
        #if self.dID % 100 == 0:
        #print('Indexing document', self.dID)
        meta = self.iterSent.get_metadata(fname)
        self.add_meta_keywords(meta)
        meta['n_words'] = self.numWords
        meta['n_sents'] = self.numSents
        if len(self.settings['languages']) > 1:
            for i in range(len(self.languages)):
                meta['n_words_' + self.languages[i]] = self.numWordsLang[i]
                meta['n_sents_' + self.languages[i]] = self.numSentsLang[i]
        self.numWords = 0
        self.numSents = 0
        self.numWordsLang = [0] * len(self.languages)
        self.numSentsLang = [0] * len(self.languages)
        try:
            self.es.index(index=self.name + '.docs',
                          doc_type='doc',
                          id=self.dID,
                          body=meta)
        except RequestError as err:
            #print('Metadata error: {0}'.format(err))
            shortMeta = {}
            if 'filename' in meta:
                shortMeta['filename'] = meta['filename']
            if 'title' in meta:
                shortMeta['title'] = meta['title']
                shortMeta['title_kw'] = meta['title']
                self.es.index(index=self.name + '.docs',
                              doc_type='doc',
                              id=self.dID,
                              body=shortMeta)
        self.dID += 1

    def index_dir(self):
        """
        Index all files from the corpus directory, sorted by their size
        in decreasing order. Such sorting helps prevent memory errors
        when indexing large corpora, as the default behavior is to load
        the whole file is into memory, and there is more free memory
        in the beginning of the process. If MemoryError occurs, the
        iterative JSON parser is used, which works much slower.
        """
        filenames = []
        for root, dirs, files in os.walk(self.corpus_dir):
            for fname in files:
                if (not ((self.settings['input_format'] == 'json'
                          and fname.lower().endswith('.json')) or
                         (self.settings['input_format'] == 'json-gzip'
                          and fname.lower().endswith('.json.gz')))):
                    continue
                fnameFull = os.path.join(root, fname)
                filenames.append((fnameFull, os.path.getsize(fnameFull)))
        if len(filenames) <= 0:
            print('There are no files in this corpus.')
            return
        for fname, fsize in sorted(filenames, key=lambda p: -p[1]):
            # print(fname, fsize)
            bulk(self.es,
                 self.iterate_sentences(fname),
                 chunk_size=200,
                 request_timeout=60)
            self.index_doc(fname)
        self.index_words()

    def compile_translations(self):
        """
        Compile flask_babel translations in ../search/web_app.
        """
        pythonPath = ''
        for p in sys.path:
            if re.search('Python3[^/\\\\]*[/\\\\]?$', p) is not None:
                pythonPath = p
                break
        if len(pythonPath) <= 0:
            pyBabelPath = 'pybabel'
        else:
            pyBabelPath = os.path.join(pythonPath, 'Scripts', 'pybabel')
        try:
            subprocess.run([pyBabelPath, 'compile', '-d', 'translations'],
                           cwd='../search/web_app',
                           check=True)
        except:
            print('Could not compile translations with ' + pyBabelPath + ' .')
        else:
            print('Interface translations compiled.')

    def load_corpus(self):
        """
        Drop the current database, if any, and load the entire corpus.
        """
        t1 = time.time()
        self.compile_translations()
        self.delete_indices()
        self.create_indices()
        self.index_dir()
        t2 = time.time()
        print('Corpus indexed in', t2 - t1, 'seconds:', self.dID, 'documents,',
              self.sID, 'sentences,', self.totalNumWords, 'words,',
              sum(len(self.wordFreqs[i]) for i in range(len(self.languages))),
              'word types (different words).')
Exemple #16
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def run_training(config_file, load_filename=""):
    # read data

    config = Config.from_json_file(config_file)
    save_dir = config.save_dir
    datafile = config.datafile
    corpus_dir = config.corpus_dir

    prepare_data = PrepareData(min_count=config.MIN_COUNT,
                               max_length=config.MAX_LENGTH)
    vocab, pairs = prepare_data.load_prepare_data(corpus_dir, datafile,
                                                  save_dir)

    # set checkpoint to load from; set to None if starting from scratch
    # load_filename = os.path.join(save_dir, model_name, corpus_name, '{}-{}_{}'.format(encoder_n_layers, decoder_n_layers, hidden_size),
    #                            '{}_checkpoint.tar'.format(checkpoint_iter))

    if load_filename:
        # if loading on the same machine the model trained on
        checkpoint = torch.load(load_filename)
        # if loading a model trained on gpu to cpu
        # checkpoint = torch.load(load_filename, map_location=torch.device('cpu'))
        encoder_sd = checkpoint["en"]
        decoder_sd = checkpoint["de"]
        encoder_optimizer_sd = checkpoint["en_opt"]
        decoder_optimizer_sd = checkpoint["de_opt"]
        embedding_sd = checkpoint["embedding"]
        vocab.__dict__ = checkpoint["voc_dict"]

    print("Building encoder and decoder ...")
    # initialize word embeddings
    embedding = nn.Embedding(vocab.num_words,
                             config.hidden_size).to(config.device)
    if load_filename:
        embedding.load_state_dict(embedding_sd)

    # initialize encoder and decoder models
    encoder = EncoderRNN(config.hidden_size, embedding,
                         config.encoder_n_layers,
                         config.dropout).to(config.device)
    decoder = LuongAttnDecoderRNN(config.attn_model, embedding,
                                  config.hidden_size, vocab.num_words,
                                  config.decoder_n_layers,
                                  config.dropout).to(config.device)

    if load_filename:
        encoder.load_state_dict(encoder_sd)
        decoder.load_state_dict(decoder_sd)

    print("Models built and ready to go.")

    #####################################
    # ensure dropout layers are in train mode
    encoder.train()
    decoder.train()

    # initilize optimizers
    print("building optimizers")
    encoder_optimizer = optim.Adam(encoder.parameters(),
                                   lr=config.learning_rate)
    decoder_optimizer = optim.Adam(decoder.parameters(),
                                   lr=config.learning_rate *
                                   config.decoder_learning_ratio)

    if load_filename:
        encoder_optimizer.load_state_dict(encoder_optimizer_sd)
        decoder_optimizer.load_state_dict(decoder_optimizer_sd)

    # run training iterations
    training_iters(config, vocab, pairs, encoder, decoder, encoder_optimizer,
                   decoder_optimizer, embedding, save_dir, load_filename)
Exemple #17
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import pandas as pd
import numpy as np
import matplotlib.pyplot as plt

from prepare_data import PrepareData
from pprint import pprint

if __name__ == "__main__":
    p = PrepareData()
    result = p.process_all_gene()
    result = sorted(result, key=lambda x: x[1], reverse=True)

    index = [x[0] for x in result]
    value = [x[1] for x in result]

    # print([index, value])
    df = pd.DataFrame(
        data=result,
        columns=["index", "value"],
    )
    df.to_csv("./result/3.csv", index=False)

    ## Plot
    plt.figure()
    plt.bar(index, value, width=.2, color='g')
    plt.title("Gene Importance Bar Image")
    plt.xlabel("Gene number")
    plt.ylabel("Gene importance")
    plt.savefig('./result/3.png')
    plt.close()
Exemple #18
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def main():
    # 数据预处理
    # dataList = []
    # for i in range(3,11):
    #     dataList.append(PrepareData())
    #     args.train_file = '/Users/wangyihao/Pycharm/transformer-simple-master_new/data/data' + str(i) + '.p'
    data = PrepareData()
    args.src_vocab = len(data.en_word_dict)
    args.tgt_vocab = len(data.cn_word_dict)
    print("src_vocab %d" % args.src_vocab)
    print("tgt_vocab %d" % args.tgt_vocab)

    # 初始化模型
    model = make_model(args.src_vocab, args.tgt_vocab, args.layers,
                       args.d_model, args.d_ff, args.h_num, args.dropout)

    if args.type == 'train':
        # 训练
        print(">>>>>>> start train")
        criterion = LabelSmoothing(args.tgt_vocab,
                                   padding_idx=0,
                                   smoothing=0.0)
        optimizer = NoamOpt(
            args.d_model, 1, 2000,
            torch.optim.Adam(model.parameters(),
                             lr=0,
                             betas=(0.9, 0.98),
                             eps=1e-9))
        train(data, model, criterion, optimizer)
        print("<<<<<<< finished train")
    elif args.type == "evaluate":  # 预测
        # 先判断模型有没有训练好(前提)
        if os.path.exists(args.save_file):
            # 加载模型
            model.load_state_dict(torch.load(args.save_file))
            # 开始预测
            print(">>>>>>> start evaluate")
            precision = evaluate(data, model)
            TP_total = precision.sum(axis=0)[0]
            FP_total = precision.sum(axis=0)[1]
            TN_total = precision.sum(axis=0)[2]
            FN_total = precision.sum(axis=0)[3]
            TPR = TP_total / (TP_total + FN_total)  #计算真正率
            TNR = TN_total / (TN_total + FP_total)  #计算真负率
            print(
                'total true positive amount: %.3f, total false negative amount: %.3f'
                % (TP_total, FN_total))
            print(
                'total true negative amount: %.3f, total false positive amount: %.3f'
                % (TN_total, FP_total))
            print('symbol within feature TPR: %.3f, delimiter TNR: %.3f' %
                  (TPR, TNR))
            print("<<<<<<< finished evaluate")
        else:
            print("Error: pleas train before evaluate")
    elif args.type == "predict":  #输入特征并预测
        if os.path.exists(args.save_file):
            # 加载模型
            model.load_state_dict(torch.load(args.save_file))
            # 开始预测
            print(">>>>>>> start predict")
            translation = predict(data, model)
            print("<<<<<<< finished predict")
    else:
        print("Error: please select type within [train / evaluate / predict]")