Open Radhu903 opened 3 years ago
C:\Users\DELL\openDiagram\physchem\python>python search_lib.py --dict activity --sect introduction method --proj activity running search main project files not available for C:\Users\DELL\openDiagram\python\diagrams\satish\cct project files not available for C:\Users\DELL\openDiagram\python\diagrams\rahul\diffprotexp project files not available for C:\Users\DELL\openVirus\miniproject\disease\1-part project files not available for C:\Users\DELL\worcester\synthesis project files not available for C:\Users\DELL\worcester\explosion Failed to read dictionary C:\Users\DELL\CEVOpen\dictionary\eoCompound\plant_compound.xml Start tag expected, '<' not found, line 1, column 1 (file:/C:/Users/DELL/CEVOpen/dictionary/eoCompound/plant_compound.xml, line 1) Failed to read dictionary C:\Users\DELL\CEVOpen\dictionary\eoPlant\Plant.xml Opening and ending tag mismatch: entry line 91 and dictionary, line 2399, column 14 (file:/C:/Users/DELL/CEVOpen/dictionary/eoPlant/Plant.xml, line 2399) Failed to read dictionary C:\Users\DELL\CEVOpen\dictionary\eoCompound\plant_compound.xml Start tag expected, '<' not found, line 1, column 1 (file:/C:/Users/DELL/CEVOpen/dictionary/eoCompound/plant_compound.xml, line 1) core dicts dict_keys(['activity', 'country', 'disease', 'plant_genus', 'organization', 'plant_part', 'invasive_plant']) commandline args dicts ['activity'] <class 'list'> sects ['introduction', 'method'] <class 'list'> projs ['activity'] <class 'list'> patterns None <class 'NoneType'> args> Namespace(dict=['activity'], sect=['introduction', 'method'], proj=['activity'], patt=None, demo=None, loglevel='foo', plot=True, nosearch=False, maxbars=25, languages=['en']) name activity ***** project C:\Users\DELL\CEVOpen\minicorpora\activity _DESC <class 'str'> introduction or background; looks for these words anywhere in file titles PROJ <class 'str'> C:\Users\DELL\CEVOpen\minicorpora\activity TREE <class 'str'> * SECTS <class 'str'> ** SUBSECT <class 'str'> *introduction* SUBSUB <class 'str'> ** FILE <class 'str'> * SUFFIX <class 'str'> xml glob C:\Users\DELL\CEVOpen\minicorpora\activity/*/**/*introduction*/**/*.xml _DESC <class 'str'> introduction or background; looks for these words anywhere in file titles PROJ <class 'str'> C:\Users\DELL\CEVOpen\minicorpora\activity TREE <class 'str'> * SECTS <class 'str'> ** SUBSECT <class 'str'> *background* SUBSUB <class 'str'> ** FILE <class 'str'> * SUFFIX <class 'str'> xml glob C:\Users\DELL\CEVOpen\minicorpora\activity/*/**/*background*/**/*.xml files 1203 ***** section_files introduction 1203 file C:\Users\DELL\CEVOpen\minicorpora\activity\PMC7210559\sections\1_body\0_1__introduction\0_title.xml findfont: Font family ['Helvetica'] not found. Falling back to DejaVu Sans. findfont: Font family ['Helvetica'] not found. Falling back to DejaVu Sans. lang: en [('antioxidant', 181), ('antifungal', 111), ('cosmetics', 15), ('analgesic', 15), ('antiseptic', 12), ('derivative', 10), ('antiprotozoal', 8), ('cytotoxicity', 7), ('antispasmodic', 5), ('perfume', 5), ('antiparasitic', 5), ('antiemetic', 4), ('anxiolytic', 4), ('fungicide', 3), ('antitussive', 3), ('diuretic', 3), ('insecticide', 2), ('phytotoxicity', 2), ('aphrodisiac', 2), ('larvicide', 2), ('irritant', 1), ('antipyretic', 1), ('immunomodulator', 1), ('anticoagulant', 1), ('bronchodilator', 1), ('anthelmintic', 1), ('sedative', 1), ('carcinogen', 1), ('choleretic', 1), ('stomachic', 1), ('astringent', 1), ('hypolipidemic', 1), ('pesticide', 1), ('anaphylactic', 1), ('adenosine', 1), ('antimalarial', 1), ('photosensitizer', 1)] _DESC <class 'str'> methods and/or materials; looks for these words anywhere in file titles PROJ <class 'str'> C:\Users\DELL\CEVOpen\minicorpora\activity TREE <class 'str'> * SECTS <class 'str'> ** SUBSECT <class 'str'> *method* SUBSUB <class 'str'> ** FILE <class 'str'> *p SUFFIX <class 'str'> xml glob C:\Users\DELL\CEVOpen\minicorpora\activity/*/**/*method*/**/*p.xml _DESC <class 'str'> methods and/or materials; looks for these words anywhere in file titles PROJ <class 'str'> C:\Users\DELL\CEVOpen\minicorpora\activity TREE <class 'str'> * SECTS <class 'str'> ** SUBSECT <class 'str'> *material* SUBSUB <class 'str'> ** FILE <class 'str'> *p SUFFIX <class 'str'> xml glob C:\Users\DELL\CEVOpen\minicorpora\activity/*/**/*material*/**/*p.xml files 3148 ***** section_files method 3148 file C:\Users\DELL\CEVOpen\minicorpora\activity\PMC7210559\sections\1_body\1_2__materials_and_methods\1_2_1__materials\1_p.xml Traceback (most recent call last): File "C:\Users\DELL\openDiagram\physchem\python\search_lib.py", line 955, in <module> main() File "C:\Users\DELL\openDiagram\physchem\python\search_lib.py", line 918, in main ami_search.run_search() File "C:\Users\DELL\openDiagram\physchem\python\search_lib.py", line 340, in run_search self.find_files_search_plot(proj, section_type) File "C:\Users\DELL\openDiagram\physchem\python\search_lib.py", line 347, in find_files_search_plot counter_dict, pattern_dict = self.search_and_count(section_files) File "C:\Users\DELL\openDiagram\physchem\python\search_lib.py", line 294, in search_and_count matches_by_amidict, matches_by_pattern = self.search(target_file) File "C:\Users\DELL\openDiagram\physchem\python\search_lib.py", line 210, in search words = TextUtil.get_words_in_section(file) File "C:\Users\DELL\openDiagram\physchem\python\text_lib.py", line 447, in get_words_in_section section.read_file(file) File "C:\Users\DELL\openDiagram\physchem\python\text_lib.py", line 251, in read_file self.sentences = [Sentence(s) for s in (nltk.sent_tokenize(self.txt))] File "C:\Users\DELL\AppData\Local\Programs\Python\Python39\lib\site-packages\nltk\tokenize\__init__.py", line 106, in sent_tokenize tokenizer = load("tokenizers/punkt/{0}.pickle".format(language)) File "C:\Users\DELL\AppData\Local\Programs\Python\Python39\lib\site-packages\nltk\data.py", line 752, in load opened_resource = _open(resource_url) File "C:\Users\DELL\AppData\Local\Programs\Python\Python39\lib\site-packages\nltk\data.py", line 877, in _open return find(path_, path + [""]).open() File "C:\Users\DELL\AppData\Local\Programs\Python\Python39\lib\site-packages\nltk\data.py", line 585, in find raise LookupError(resource_not_found) LookupError: ********************************************************************** Resource ←[93mpunkt←[0m not found. Please use the NLTK Downloader to obtain the resource: ←[31m>>> import nltk >>> nltk.download('punkt') ←[0m For more information see: https://www.nltk.org/data.html Attempted to load ←[93mtokenizers/punkt/english.pickle←[0m Searched in: - 'C:\\Users\\DELL/nltk_data' - 'C:\\Users\\DELL\\AppData\\Local\\Programs\\Python\\Python39\\nltk_data' - 'C:\\Users\\DELL\\AppData\\Local\\Programs\\Python\\Python39\\share\\nltk_data' - 'C:\\Users\\DELL\\AppData\\Local\\Programs\\Python\\Python39\\lib\\nltk_data' - 'C:\\Users\\DELL\\AppData\\Roaming\\nltk_data' - 'C:\\nltk_data' - 'D:\\nltk_data' - 'E:\\nltk_data' - '' **********************************************************************