def __verifyRemovalOfInTextExpansions(self, article_for_testing, acronyms):
expander = Expander_fromText()
for acronym in acronyms:
for pattern in expander.definition_patterns(acronym):
if(len(pattern.findall(article_for_testing)) > 0):
errorString = "Verification of text expansion removal failed:\nAcronym: " +\
acronym + "\nText:\n" + article_for_testing
common_logger.error(errorString)
raise RuntimeError(errorString)
if acronym not in article_for_testing:
errorMessage = "Acronym removed from text while cleaning:\nAcronym: " +\
acronym + "\nText:\n" + article_for_testing
common_logger.error(errorMessage)
raise RuntimeError(errorMessage)
def _createArticleAndAcronymDB():
acronymExpander = Expander_fromText_v2()
articleDB = {}
acronymDB = {}
CUID_to_expansion = {}
for fileName in os.listdir(folder_msh_arff):
filePath = os.path.join(folder_msh_arff, fileName)
file_reader = arff.Reader(open(filePath, "rb"))
# the iterator needs to be called for the self.relation part to be
# initialized
lines = list(file_reader)
cuids = file_reader.relation.strip().split("_")
# storing all acronyms as uppercase values
acronym = _fileNameToAcronym(fileName).upper()
cuid_and_pmid = []
for line in lines:
pmid = unicode(line.PMID)
text = TextTools.toUnicode(line.citation)
cuid = cuids[_classToIndex(line["class"])]
textWithoutMarkup = _removeMarkup(text)
if (cuid not in CUID_to_expansion):
acronymExpansions = []
acronymExpansions = acronymExpander.expand(
acronym, acronymExpansions, textWithoutMarkup)
if (len(acronymExpansions) != 0 and
acronymExpansions[0].expansion != acronym):
CUID_to_expansion[cuid] = acronymExpansions[0].expansion
if (pmid not in articleDB):
articleDB[pmid] = textWithoutMarkup
cuid_and_pmid.append([cuid, pmid])
if (acronym in acronymDB):
common_logger.error("acronym already present in acronymDB")
else:
acronymDB[acronym] = []
for cuid, pmid in cuid_and_pmid:
if (cuid in CUID_to_expansion):
acronymDB[acronym].append([CUID_to_expansion[cuid], pmid, 0])
else:
common_logger.error(
"Expansion not found for CUID %s of %s" % (cuid, acronym))
acronymDB[acronym].append([cuid, pmid, 0])
return acronymDB, articleDB
def internal_server_error(e):
common_logger.error(e)
return render_template(string_constants.file_errorpage), 500