def load_corpus(self, corenlpserver, process=True):
# self.path is the base directory of the files of this corpus
trainfiles = [self.path + '/' + f for f in os.listdir(self.path) if f.endswith('.txt')]
total = len(trainfiles)
widgets = [pb.Percentage(), ' ', pb.Bar(), ' ', pb.AdaptiveETA(), ' ', pb.Timer()]
pbar = pb.ProgressBar(widgets=widgets, maxval=total, redirect_stdout=True).start()
time_per_abs = []
for current, f in enumerate(trainfiles):
#logging.debug('%s:%s/%s', f, current + 1, total)
print '{}:{}/{}'.format(f, current + 1, total)
did = f.split(".")[0]
t = time.time()
with open(f, 'r') as txt:
doctext = txt.read()
newdoc = Document(doctext, process=False, did=did)
newdoc.sentence_tokenize("biomedical")
if process:
newdoc.process_document(corenlpserver, "biomedical")
self.documents[newdoc.did] = newdoc
abs_time = time.time() - t
time_per_abs.append(abs_time)
#logging.info("%s sentences, %ss processing time" % (len(newdoc.sentences), abs_time))
pbar.update(current+1)
pbar.finish()
abs_avg = sum(time_per_abs)*1.0/len(time_per_abs)
logging.info("average time per abstract: %ss" % abs_avg)
def load_corpus(self, corenlpserver, process=True):
trainfiles = [self.path + '/' + f for f in os.listdir(self.path)]
total = len(trainfiles)
widgets = [pb.Percentage(), ' ', pb.Bar(), ' ', pb.AdaptiveETA(), ' ', pb.Timer()]
pbar = pb.ProgressBar(widgets=widgets, maxval=total, redirect_stdout=True).start()
time_per_abs = []
for current, f in enumerate(trainfiles):
#logging.debug('%s:%s/%s', f, current + 1, total)
print '{}:{}/{}'.format(f, current + 1, total)
did = f
t = time.time()
with open(f, 'r') as f:
article = "<Article>" + f.read() + "</Article>"
soup = BeautifulSoup(article, 'xml')
#doc = soup.find_all("article")
title = soup.ArticleTitle.get_text()
abstract = soup.AbstractText.get_text()
doc_text = title + " " + abstract
newdoc = Document(doc_text, process=False, did=did)
newdoc.sentence_tokenize("biomedical")
newdoc.process_document(corenlpserver, "biomedical")
#logging.info(len(newdoc.sentences))
self.documents[newdoc.did] = newdoc
abs_time = time.time() - t
time_per_abs.append(abs_time)
logging.debug("%s sentences, %ss processing time" % (len(newdoc.sentences), abs_time))
pbar.update(current)
pbar.finish()
abs_avg = sum(time_per_abs)*1.0/len(time_per_abs)
logging.info("average time per abstract: %ss" % abs_avg)
def load_corpus(self, corenlpserver, process=True):
# self.path is the base directory of the files of this corpus
trainfiles = [self.path + '/' + f for f in os.listdir(self.path) if f.endswith('.txt')]
total = len(trainfiles)
widgets = [pb.Percentage(), ' ', pb.Bar(), ' ', pb.AdaptiveETA(), ' ', pb.Timer()]
pbar = pb.ProgressBar(widgets=widgets, maxval=total, redirect_stdout=True).start()
time_per_abs = []
for current, f in enumerate(trainfiles):
#logging.debug('%s:%s/%s', f, current + 1, total)
print ('{}:{}/{}'.format(f, current + 1, total))
did = f.split(".")[0].split("/")[-1]
t = time.time()
with codecs.open(f, 'r', 'utf-8') as txt:
doctext = txt.read()
doctext = doctext.replace("\n", " ")
newdoc = Document(doctext, process=False, did=did)
newdoc.sentence_tokenize("biomedical")
if process:
newdoc.process_document(corenlpserver, "biomedical")
self.documents[newdoc.did] = newdoc
abs_time = time.time() - t
time_per_abs.append(abs_time)
#logging.info("%s sentences, %ss processing time" % (len(newdoc.sentences), abs_time))
pbar.update(current+1)
pbar.finish()
abs_avg = sum(time_per_abs)*1.0/len(time_per_abs)
logging.info("average time per abstract: %ss" % abs_avg)
def load_corpus(self, corenlpserver, process=True):
"""Load the CHEMDNER corpus file on the dir element"""
# open filename and parse lines
total_lines = sum(1 for line in open(self.path))
widgets = [pb.Percentage(), ' ', pb.Bar(), ' ', pb.ETA(), ' ', pb.Timer()]
pbar = pb.ProgressBar(widgets=widgets, maxval=total_lines).start()
n_lines = 1
time_per_abs = []
with io.open(self.path, 'r', encoding="utf-8") as inputfile:
for line in inputfile:
t = time.time()
# each line is PMID title abs
tsv = line.split('\t')
doctext = tsv[1].strip().replace("<", "(").replace(">", ")") + " "
doctext += tsv[2].strip().replace("<", "(").replace(">", ")")
newdoc = Document(doctext, process=False,
did=tsv[0], title=tsv[1].strip() + ".")
newdoc.sentence_tokenize("biomedical")
if process:
newdoc.process_document(corenlpserver, "biomedical")
self.documents[newdoc.did] = newdoc
abs_time = time.time() - t
time_per_abs.append(abs_time)
pbar.update(n_lines)
n_lines += 1
pbar.finish()
abs_avg = sum(time_per_abs)*1.0/len(time_per_abs)
logging.info("average time per abstract: %ss" % abs_avg)
def load_corpus(self, corenlpserver, process=True):
trainfiles = [self.path + '/' + f for f in os.listdir(self.path)]
total = len(trainfiles)
widgets = [pb.Percentage(), ' ', pb.Bar(), ' ', pb.AdaptiveETA(), ' ', pb.Timer()]
pbar = pb.ProgressBar(widgets=widgets, maxval=total, redirect_stdout=True).start()
time_per_abs = []
for current, f in enumerate(trainfiles):
#logging.debug('%s:%s/%s', f, current + 1, total)
print '{}:{}/{}'.format(f, current + 1, total)
did = f
t = time.time()
with open(f, 'r') as f:
article = "<Article>" + f.read() + "</Article>"
soup = BeautifulSoup(article, 'xml')
#doc = soup.find_all("article")
title = soup.ArticleTitle.get_text()
abstract = soup.AbstractText.get_text()
doc_text = title + " " + abstract
newdoc = Document(doc_text, process=False, did=did)
newdoc.sentence_tokenize("biomedical")
newdoc.process_document(corenlpserver, "biomedical")
#logging.info(len(newdoc.sentences))
self.documents[newdoc.did] = newdoc
abs_time = time.time() - t
time_per_abs.append(abs_time)
logging.debug("%s sentences, %ss processing time" % (len(newdoc.sentences), abs_time))
pbar.update(current)
pbar.finish()
abs_avg = sum(time_per_abs)*1.0/len(time_per_abs)
logging.info("average time per abstract: %ss" % abs_avg)
def load_corpus(self, corenlpserver, process=True):
"""Load the CHEMDNER corpus file on the dir element"""
# open filename and parse lines
total_lines = sum(1 for line in open(self.path))
widgets = [pb.Percentage(), ' ', pb.Bar(), ' ', pb.ETA(), ' ', pb.Timer()]
pbar = pb.ProgressBar(widgets=widgets, maxval=total_lines).start()
n_lines = 1
time_per_abs = []
with io.open(self.path, 'r', encoding="utf-8") as inputfile:
for line in inputfile:
t = time.time()
# each line is PMID title abs
tsv = line.split('\t')
doctext = tsv[1].strip().replace("<", "(").replace(">", ")").replace(". ", ", ") + ". "
doctext += tsv[2].strip().replace("<", "(").replace(">", ")")
newdoc = Document(doctext, process=False,
did=tsv[0], title=tsv[1].strip() + ".")
newdoc.sentence_tokenize("biomedical")
if process:
newdoc.process_document(corenlpserver, "biomedical")
self.documents[newdoc.did] = newdoc
abs_time = time.time() - t
time_per_abs.append(abs_time)
pbar.update(n_lines)
n_lines += 1
pbar.finish()
abs_avg = sum(time_per_abs)*1.0/len(time_per_abs)
logging.info("average time per abstract: %ss" % abs_avg)
def generate_corpus(self, text):
"""
Create a corpus object from the input text.
:param text:
:return:
"""
test_corpus = Corpus("")
newdoc = Document(text, process=False, did="d0", title="Test document")
newdoc.sentence_tokenize("biomedical")
newdoc.process_document(self.corenlp, "biomedical")
test_corpus.documents["d0"] = newdoc
return test_corpus
def create_sentences(self, doctag, text):
# Create sentence entries based on text from document doctag
cur = self.db_conn.cursor()
newdoc = Document(text, process=False,
did=doctag)
newdoc.sentence_tokenize("biomedical")
for i, sentence in enumerate(newdoc.sentences):
corenlpres = sentence.process_sentence(self.corenlp)
query = """INSERT INTO sentence(senttag, doctag, senttext, sentoffset, corenlp) VALUES (%s, %s, %s, %s, %s);"""
try:
cur.execute(query, (sentence.sid, doctag, sentence.text.encode("utf8"), sentence.offset,
str(corenlpres).encode("utf8")))
self.db_conn.commit()
#inserted_id = cur.lastrowid
#return str(inserted_id)
except MySQLdb.MySQLError as e:
self.db_conn.rollback()
logging.debug(e)
