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Julien Michel authored
STY: Change ITK_OVERRIDE for override in whole code (find Modules -type f -exec sed -i 's/ITK_OVERRIDE/override/g' {} +)756ee5dc
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import os,glob,shutil,sys,time
from pathlib import Path
import pandas as pd
home = str(Path.home())
class BiotexWrapper():
"""
Wrapper to execute and returned the result from the Biotex program
See more about Biotex at: http://tubo.lirmm.fr:8080/biotex/index.jsp
"""
def __init__(self,
biotex_jar_path = os.path.join(os.path.dirname(__file__),"Biotex.jar"),
pattern_path = os.path.join(os.path.dirname(__file__),"patterns"),
dataset_src = os.path.join(os.path.dirname(__file__),"dataSetReference") ,
stopwords_src = os.path.join(os.path.dirname(__file__),"stopWords"),
treetagger_src = os.path.join(home,".tree-tagger/"),
type_of_terms = "all",
language = "french",
score = "F-TFIDF-C_M",
patron_number = "3"):
"""
Constructor
Parameters
----------
biotex_jar_path : str, optional
Filepath of Biotex jar, by default os.path.join(os.path.dirname(__file__),"Biotex.jar")
pattern_path : str, optional
Directory that contains pre-defined patterns, by default os.path.join(os.path.dirname(__file__),"patterns")
dataset_src : src, optional
FilePath of datasets used by Biotex, by default os.path.join(os.path.dirname(__file__),"dataSetReference")
stopwords_src : str, optional
Path of the directory that contains stopwords for each language, by default os.path.join(os.path.dirname(__file__),"stopWords")
treetagger_src : str, optional
Path of the directory that contains TreeTagger, by default os.path.join(home,".tree-tagger/")
type_of_terms : str, optional
number of terms you want to extract, by default "all"
language : str, optional
language of the data, by default "french"
score : str, optional
score used to sort the extracted term, by default "F-TFIDF-C_M"
patron_number : str, optional
number of pattern used to extract terms, by default "3"
"""
self.biotexJarPath=biotex_jar_path
self.configuration={
"patternsSrc":pattern_path,
"datasetSrc":dataset_src,
"stopwordsSrc":stopwords_src,
"treetaggerSrc":treetagger_src,
"typeOfTerms":type_of_terms,
"language":language,
"score":score,
"patronNumber":patron_number
}
self.write_conf(self.configuration)
self.output_data=None
def create_corpus_from_txt(self,list_of_text : list, outputfn="output.txt"):
"""
Transform a corpus (based on a list of str) into BiotexFormat
Parameters
----------
list_of_text : list
list of stre
outputfn : str, optional
output filename (the default is "output.txt")
"""
corpus=""
sep="\n##########END##########\n"
corpus = sep.join(list_of_text)
open(outputfn,'w').write((corpus+sep).strip())
def write_conf(self,confDict):
"""
Create the configuration file to execute Biotex
"""
f=open("configuration.txt",'w')
for key in confDict.keys():
f.write("{0}={1}\n".format(key,confDict[key]))
f.close()
def extract_terminology(self,inputFile,nbGram="ALL"):
"""
Execute and extract the result returned by Biotex
"""
if isinstance(nbGram,str):
if nbGram != "ALL":
print("Error : Except 'ALL' value, nbGram args in extractTerminology method can't take string arg !!!\nAvailable values: 'ALL',1,2,3,4")
return False
if isinstance(nbGram,int):
if nbGram > 4 or nbGram < 0:
print("Error : nbGram value : {0} is forbidden!\nAvailable values: 'ALL',1,2,3,4 ".format(nbGram))
return False
#if not isinstance(nbGram,str) or not isinstance(nbGram,int):
#print("Error: Wrong args type :{0}!\nAvailable values: 'ALL',1,2,3,4 ".format(type(nbGram)))
#return False
debut=time.time()
status=os.system("java -Xms6g -Xmx10g -jar {0} {1}".format(self.biotexJarPath,inputFile))
print("Done in {0} sec".format(time.time()-debut))
if status == 1 :
print("Biotex java program has crashed !")
return False
if not os.path.exists("output"):
os.makedirs("output")
if isinstance(nbGram,int):
output=open("output/t{0}gram.txt".format(nbGram),'r').read()
else:
output=open("output/ALL_gram.txt",'r').read()
#output=open("output/{0}{1}gram.txt".format('t' if isinstance(nbGram,int) else '',str(nbGram)+"_" if ),'r').read()
data=[]
for line in output.split("\n"):
parsed=line.split(";")
if len(parsed) == 3:
parsed[1]=int(parsed[1])
parsed[2]=float(parsed[2])
data.append(parsed)
shutil.rmtree('output')
for f in glob.glob("to_tag_*.txt"):
os.remove(f)
self.output_data=data
return self.output_data
def terminology(self, corpus):
try:
self.create_corpus_from_txt(corpus)
except:
raise Exception("Error while creating file !")
return pd.DataFrame(self.extract_terminology("output.txt"), columns = "term in_umls rank".split())
if __name__ == '__main__':
import argparse
parser= argparse.ArgumentParser()
parser.add_argument("input",help="Your Biotex input filename")
parser.add_argument('-s',"--sizeOfGram",help="Gram size of the term you want to extract")
parser.add_argument('-o',"--output",help="Output filename")
parser.add_argument('-d',"--debug",action="store_true",help="debug activated")
args=parser.parse_args()
if args.debug:
print(args)
wrap=BiotexWrapper()
if args.sizeOfGram:
if args.sizeOfGram != 'ALL':
try:
sGram=int(args.sizeOfGram)
except:
sGram=args.sizeOfGram
else:sGram="ALL"
data=wrap.extract_terminology(args.input,nbGram=sGram)
out_=open((args.output if args.output else "GRAM_ALL.txt"),'w')
for d in data:
#print(d)
#print("\t".join(d))
out_.write("\t".join(map(str, d))+"\n")
out_.close()
#print(test)