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rename to nbs/benchmark/covid_data/temp/sample9997.txt diff --git a/nbs/banchmark/covid_data/temp/sample9998.txt b/nbs/benchmark/covid_data/temp/sample9998.txt similarity index 100% rename from nbs/banchmark/covid_data/temp/sample9998.txt rename to nbs/benchmark/covid_data/temp/sample9998.txt diff --git a/nbs/banchmark/covid_data/temp/sample9999.txt b/nbs/benchmark/covid_data/temp/sample9999.txt similarity index 100% rename from nbs/banchmark/covid_data/temp/sample9999.txt rename to nbs/benchmark/covid_data/temp/sample9999.txt diff --git a/spannerlib/_modidx.py b/spannerlib/_modidx.py index 3bb598c5..dd308de0 100644 --- a/spannerlib/_modidx.py +++ b/spannerlib/_modidx.py @@ -13,27 +13,27 @@ 'spannerlib/adding_inference_rules_to_term_graph.py'), 'spannerlib.adding_inference_rules_to_term_graph.AddRulesToTermGraph.run_pass': ( 'adding_inference_rules_to_term_graph.html#addrulestotermgraph.run_pass', 'spannerlib/adding_inference_rules_to_term_graph.py')}, - 'spannerlib.banchmark.covid': { 'spannerlib.banchmark.covid.AggDocumentTags': ( 'banchmark/covid.html#aggdocumenttags', + 'spannerlib.banchmark.covid': { 'spannerlib.banchmark.covid.AggDocumentTags': ( 'benchmark/covid.html#aggdocumenttags', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.LemmaFromList': ( 'banchmark/covid.html#lemmafromlist', + 'spannerlib.banchmark.covid.LemmaFromList': ( 'benchmark/covid.html#lemmafromlist', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.LemmaFromList.__call__': ( 'banchmark/covid.html#lemmafromlist.__call__', + 'spannerlib.banchmark.covid.LemmaFromList.__call__': ( 'benchmark/covid.html#lemmafromlist.__call__', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.LemmaFromList.__init__': ( 'banchmark/covid.html#lemmafromlist.__init__', + 'spannerlib.banchmark.covid.LemmaFromList.__init__': ( 'benchmark/covid.html#lemmafromlist.__init__', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.PosFromList': ( 'banchmark/covid.html#posfromlist', + 'spannerlib.banchmark.covid.PosFromList': ( 'benchmark/covid.html#posfromlist', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.PosFromList.__call__': ( 'banchmark/covid.html#posfromlist.__call__', + 'spannerlib.banchmark.covid.PosFromList.__call__': ( 'benchmark/covid.html#posfromlist.__call__', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.PosFromList.__init__': ( 'banchmark/covid.html#posfromlist.__init__', + 'spannerlib.banchmark.covid.PosFromList.__init__': ( 'benchmark/covid.html#posfromlist.__init__', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.agg_mention': ( 'banchmark/covid.html#agg_mention', + 'spannerlib.banchmark.covid.agg_mention': ( 'benchmark/covid.html#agg_mention', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.rewrite': ( 'banchmark/covid.html#rewrite', + 'spannerlib.banchmark.covid.rewrite': ( 'benchmark/covid.html#rewrite', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.rewrite_docs': ( 'banchmark/covid.html#rewrite_docs', + 'spannerlib.banchmark.covid.rewrite_docs': ( 'benchmark/covid.html#rewrite_docs', 'spannerlib/banchmark/covid.py'), - 'spannerlib.banchmark.covid.split_sentence': ( 'banchmark/covid.html#split_sentence', + 'spannerlib.banchmark.covid.split_sentence': ( 'benchmark/covid.html#split_sentence', 'spannerlib/banchmark/covid.py')}, 'spannerlib.data_types': { 'spannerlib.data_types.AGGFunction': ( 'primitive_data_types.html#aggfunction', 'spannerlib/data_types.py'), diff --git a/spannerlib/banchmark/covid.py b/spannerlib/banchmark/covid.py index b5ba7e2d..3d96e8ca 100644 --- a/spannerlib/banchmark/covid.py +++ b/spannerlib/banchmark/covid.py @@ -1,4 +1,4 @@ -# AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/banchmark/001_covid.ipynb. +# AUTOGENERATED! DO NOT EDIT! File to edit: ../../nbs/benchmark/001_covid.ipynb. # %% auto 0 __all__ = ['VERSION', 'sess', 'nlp', 'slog_file', 'input_dir', 'data_dir', 'lemma_list', 'lemmatizer', 'pos_annotator', @@ -7,7 +7,7 @@ 'section_delimeter_pattern', 'doc_tags', 'paths', 'classification', 'split_sentence', 'LemmaFromList', 'PosFromList', 'rewrite', 'rewrite_docs', 'agg_mention', 'AggDocumentTags'] -# %% ../../nbs/banchmark/001_covid.ipynb 3 +# %% ../../nbs/benchmark/001_covid.ipynb 3 # importing dependencies import re import csv @@ -39,13 +39,13 @@ nlp = spacy.load("en_core_web_sm") -# %% ../../nbs/banchmark/001_covid.ipynb 5 +# %% ../../nbs/benchmark/001_covid.ipynb 5 # configurations slog_file = Path('covid_data/covid_logic.pl') input_dir = Path('covid_data/sample_inputs') data_dir = Path('covid_data/rules_data') -# %% ../../nbs/banchmark/001_covid.ipynb 6 +# %% ../../nbs/benchmark/001_covid.ipynb 6 def split_sentence(text): """ Splits a text into individual sentences. using spacy's sentence detection. @@ -62,7 +62,7 @@ def split_sentence(text): yield Span(text,start,end) start = end + 1 -# %% ../../nbs/banchmark/001_covid.ipynb 7 +# %% ../../nbs/benchmark/001_covid.ipynb 7 class LemmaFromList(): def __init__(self,lemma_list): self.lemma_list = lemma_list @@ -82,7 +82,7 @@ def __call__(self,text): lemma_list = (data_dir/'lemma_words.txt').read_text().split() lemmatizer = LemmaFromList(lemma_list) -# %% ../../nbs/banchmark/001_covid.ipynb 8 +# %% ../../nbs/benchmark/001_covid.ipynb 8 class PosFromList(): def __init__(self,pos_list): self.pos_list = pos_list @@ -96,7 +96,7 @@ def __call__(self,text): pos_annotator = PosFromList(["NOUN", "PROPN", "PRON", "ADJ"]) -# %% ../../nbs/banchmark/001_covid.ipynb 9 +# %% ../../nbs/benchmark/001_covid.ipynb 9 if VERSION in ["SPANNERFLOW", "SPANNERFLOW_PYTHON_IE"]: sess.register('split_sentence',split_sentence,[Span],[Span]) sess.register('pos',pos_annotator,[Span],[Span,str]) @@ -106,7 +106,7 @@ def __call__(self,text): sess.register('pos',pos_annotator,[str],[Span,str]) sess.register('lemma',lemmatizer,[str],[Span,str]) -# %% ../../nbs/banchmark/001_covid.ipynb 10 +# %% ../../nbs/benchmark/001_covid.ipynb 10 def rewrite(text,span_label_pairs): """rewrites a string given a dataframe with spans and the string to rewrite them to assumes that the spans belong to the text @@ -133,7 +133,7 @@ def rewrite(text,span_label_pairs): return rewritten_text -# %% ../../nbs/banchmark/001_covid.ipynb 11 +# %% ../../nbs/benchmark/001_covid.ipynb 11 def rewrite_docs(docs,span_label,new_version): """Given a dataframe of documents of the form (path,doc,version) and a dataframe of spans to rewrite of the form (path,word,from_span,to_tag), rewrites the documents and returns a new dataframe of the form @@ -149,7 +149,7 @@ def rewrite_docs(docs,span_label,new_version): return pd.DataFrame(new_tuples,columns=['P','D','V']) -# %% ../../nbs/banchmark/001_covid.ipynb 12 +# %% ../../nbs/benchmark/001_covid.ipynb 12 sess.import_rel("ConceptTagRules",data_dir/"concept_tags_rules.csv" , delim=",") sess.import_rel("TargetTagRules",data_dir/"target_rules.csv",delim=",") sess.import_rel("SectionTags",data_dir/"section_tags.csv",delim=",") @@ -160,7 +160,7 @@ def rewrite_docs(docs,span_label,new_version): sess.import_rel("NextSentencePostprocessPatternRules",data_dir/'postprocess_pattern_next_sentence_rules.csv',delim=',') -# %% ../../nbs/banchmark/001_covid.ipynb 13 +# %% ../../nbs/benchmark/001_covid.ipynb 13 from glob import glob file_paths = [Path(p) for p in glob(str(input_dir/'*.txt'))] raw_docs = pd.DataFrame([ @@ -173,7 +173,7 @@ def rewrite_docs(docs,span_label,new_version): sess.import_rel('Docs',raw_docs) raw_docs -# %% ../../nbs/banchmark/001_covid.ipynb 15 +# %% ../../nbs/benchmark/001_covid.ipynb 15 lemma_tags = sess.export('?Lemmas(P,D,W,L)') lemma_docs = rewrite_docs(raw_docs,lemma_tags,'lemma') if VERSION in ["SPANNERFLOW", "SPANNERFLOW_PYTHON_IE"]: @@ -182,7 +182,7 @@ def rewrite_docs(docs,span_label,new_version): sess.import_rel('Docs',lemma_docs) -# %% ../../nbs/banchmark/001_covid.ipynb 17 +# %% ../../nbs/benchmark/001_covid.ipynb 17 lemma_concept_matches = sess.export('?LemmaConceptMatches(Path,Doc,Span,Label)') lemma_concepts = rewrite_docs(lemma_docs,lemma_concept_matches,'lemma_concept') if VERSION in ["SPANNERFLOW", "SPANNERFLOW_PYTHON_IE"]: @@ -190,7 +190,7 @@ def rewrite_docs(docs,span_label,new_version): else: sess.import_rel('Docs',lemma_concepts) -# %% ../../nbs/banchmark/001_covid.ipynb 20 +# %% ../../nbs/benchmark/001_covid.ipynb 20 pos_concept_matches = sess.export('?PosConceptMatches(P,D,W,L)') pos_concept_docs = rewrite_docs(lemma_concepts,pos_concept_matches,'pos_concept') if VERSION in ["SPANNERFLOW", "SPANNERFLOW_PYTHON_IE"]: @@ -198,7 +198,7 @@ def rewrite_docs(docs,span_label,new_version): else: sess.import_rel('Docs',pos_concept_docs) -# %% ../../nbs/banchmark/001_covid.ipynb 22 +# %% ../../nbs/benchmark/001_covid.ipynb 22 target_matches = sess.export('?TargetMatches(P,D,W,L)') target_rule_docs = rewrite_docs(pos_concept_docs,target_matches,'target_concept') if VERSION in ["SPANNERFLOW", "SPANNERFLOW_PYTHON_IE"]: @@ -206,16 +206,16 @@ def rewrite_docs(docs,span_label,new_version): else: sess.import_rel('Docs',target_rule_docs) -# %% ../../nbs/banchmark/001_covid.ipynb 23 +# %% ../../nbs/benchmark/001_covid.ipynb 23 section_tags = pd.read_csv(data_dir/'section_tags.csv',names=['literal','tag']) -# %% ../../nbs/banchmark/001_covid.ipynb 24 +# %% ../../nbs/benchmark/001_covid.ipynb 24 # we will programatically build a regex that matches all the section patterns section_delimeter_pattern = section_tags['literal'].str.cat(sep='|') sess.import_var('section_delimeter_pattern',section_delimeter_pattern) section_delimeter_pattern -# %% ../../nbs/banchmark/001_covid.ipynb 33 +# %% ../../nbs/benchmark/001_covid.ipynb 33 def agg_mention(group): """ aggregates attribute groups of covid spans @@ -251,10 +251,10 @@ def AggDocumentTags(group): sess.register_agg('agg_mention',agg_mention,[str],[str]) sess.register_agg('agg_doc_tags',AggDocumentTags,[str],[str]) -# %% ../../nbs/banchmark/001_covid.ipynb 35 +# %% ../../nbs/benchmark/001_covid.ipynb 35 doc_tags = sess.export('?DocumentTags(P,T)') -# %% ../../nbs/banchmark/001_covid.ipynb 36 +# %% ../../nbs/benchmark/001_covid.ipynb 36 paths = pd.DataFrame([p.name for p in file_paths],columns=['P']) classification = paths.merge(doc_tags,on='P',how='outer') classification['T']=classification['T'].fillna('UNK')