def test_main(self, mock_remove_entity_overlapping, mock_analyze_sentence):
article_data_sources = [MockDataSource(), MockDataSource()]
bacteria_catalog = MockCatalog("a")
nutrients_catalog = MockCatalog("b")
diseases_catalog = MockCatalog("c")
food_catalog = MockCatalog("d")
sentence_parser = StanfordSentenceParser(stanford_dependency_parser=None, stanford_tokenizer=False)
sentence_parser.parse_sentence = MagicMock()
sentence_parser.parse_sentence.return_value = ["yeah"]
constants.logger.info("asdasd")
main(article_data_sources, sentence_parser,
tokenizer=None, pattern_finder=None, writers=[])
do_nothing_analyzer = DoNothingSentenceAnalyzer()
analyzer = SentenceAnalyzer()
sentence_finder = SentenceFinder([], do_nothing_parser, do_nothing_analyzer, all_bacteria_catalog, [BACTERIA_TAG])
nxml_article_data_source = NxmlFreeArticleDataSource(articles_folder=nxml_articles_dir)
medline_article_data_source = MedlineAbstractsArticleDataSource(medline_file=abstracts_dir)
libgen_article_data_source = LibgenTxtArticleDataSource(libgen_folder=libgen_texts_dir)
with open(verb_ontollogy_path) as f:
verb_ontology = eval("".join(f.readlines()))
lancaster_stemmer = LancasterStemmer()
pattern_finder = PatternFinder(verb_ontology, lancaster_stemmer)
article_data_sources = [nxml_article_data_source, libgen_article_data_source, medline_article_data_source]
output_dir = get_output_dir_path()
csv_path = get_csv_path()
csv_writer = CsvWriter(csv_path)
pkl_writer = PklWriter(output_dir)
log_writer = LogWriter()
main(
article_data_sources,
writers=[csv_writer, log_writer],
sentence_finder=sentence_finder,
data_sources_to_skip=data_sources_to_skip_number,
sentences_to_skip=sentences_to_skip_number,
)