Full text evaluation

[bsantan]

Added support for full text and abstract evaluation. To test:

1. python wikipathways_literature_terms_generation.py
2. python wikipathways_literature_comparison_evaluations.py --knowledge-graph pkl --input-type annotated_diagram --wikipathways "['WP4535']" --enable-skipping True

[lagillenwater]

I got this error: Traceback (most recent call last): File "/Users/lucas/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/Projects/Cartoomics/wikipathw ays_literature_terms_generation.py", line 184, in <module> main() File "/Users/lucas/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/Projects/Cartoomics/wikipathw ays_literature_terms_generation.py", line 160, in main literature_annotations_df,guiding_term_skipped_nodes = generate_abstract_file_concept_annotations(id_file, g.labels_all,enable_skipping) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/lucas/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/Projects/Cartoomics/wikipathw ays_literature_terms_generation.py", line 32, in generate_abstract_file_concept_annotations id_df = pd.read_csv(file,header=None,sep='\t') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/r eaders.py", line 948, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/r eaders.py", line 611, in _read parser = TextFileReader(filepath_or_buffer, **kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/r eaders.py", line 1448, in __init__ self._engine = self._make_engine(f, self.engine) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/r eaders.py", line 1705, in _make_engine self.handles = get_handle( ^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/common.py ", line 863, in get_handle handle = open( ^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/Users/lucas/Library/CloudStorage/OneDrive-TheUnivers ityofColoradoDenver/Projects/Cartoomics/Wikipathways_Text_Annotation/Concept_Annotations_full_text/PMC6103457. bionlp'

Were the full text annotations added to the PR?

[lagillenwater]

New error: (Cartoomics) lucas@Lucass-MacBook-Pro Cartoomics % python wikipathways_literature_terms_generation.py Traceback (most recent call last): File "/Users/lucas/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/Projects/Cartoomics/wikipathways_literature_terms_generation.py", line 184, in <module> main() File "/Users/lucas/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/Projects/Cartoomics/wikipathways_literature_terms_generation.py", line 160, in main literature_annotations_df,guiding_term_skipped_nodes = generate_abstract_file_concept_annotations(id_file,g.labels_all,enable_skipping) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Users/lucas/Library/CloudStorage/OneDrive-TheUniversityofColoradoDenver/Projects/Cartoomics/wikipathways_literature_terms_generation.py", line 32, in generate_abstract_file_conc ept_annotations id_df = pd.read_csv(file,header=None,sep='\t') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 948, in read_csv return _read(filepath_or_buffer, kwds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 617, in _read return parser.read(nrows) ^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1748, in read ) = self._engine.read( # type: ignore[attr-defined] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/homebrew/Caskroom/miniconda/base/envs/Cartoomics/lib/python3.11/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 234, in read chunks = self._reader.read_low_memory(nrows) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "parsers.pyx", line 843, in pandas._libs.parsers.TextReader.read_low_memory File "parsers.pyx", line 904, in pandas._libs.parsers.TextReader._read_rows File "parsers.pyx", line 879, in pandas._libs.parsers.TextReader._tokenize_rows File "parsers.pyx", line 890, in pandas._libs.parsers.TextReader._check_tokenize_status File "parsers.pyx", line 2058, in pandas._libs.parsers.raise_parser_error pandas.errors.ParserError: Error tokenizing data. C error: Expected 3 fields in line 863, saw 4