def assign_rec_temp(article):
# find a sentence that mentions recording and temperature or degree celsius
full_text_ob = article.articlefulltext_set.all()[0]
ft = full_text_ob.get_content()
methods_tag = getMethodsTag(ft, article)
if methods_tag is None:
print (article.pmid, article.title, article.journal)
else:
text = re.sub('\s+', ' ', methods_tag.text)
temp_dict_list = []
sents = nltk.sent_tokenize(text)
for s in sents:
# print s.encode("iso-8859-15", "replace")
if celsius_re.findall(s):
# print article.pk
# print s.encode("iso-8859-15", "replace")
degree_ind = s.rfind(u'°C')
min_sent_ind = 0
max_sent_ind = len(s)
degree_close_str = s[np.maximum(min_sent_ind, degree_ind-20):np.minimum(max_sent_ind, degree_ind+1)]
retDict = resolve_data_float(degree_close_str)
if 'value' in retDict:
temp_dict_list.append(retDict)
elif room_temp_re.findall(s):
# print article.pk
# print s.encode("iso-8859-15", "replace")
retDict = {'value':22.0, 'max_range' : 24.0, 'min_range': 20.0}
temp_dict_list.append(retDict)
if len(temp_dict_list) > 0:
# print temp_dict_list
temp_dict_fin = validate_temp_list(temp_dict_list)
# print temp_dict_fin
if temp_dict_fin:
min_range = None
max_range = None
stderr = None
if 'min_range' in temp_dict_fin:
min_range = temp_dict_fin['min_range']
if 'max_range' in temp_dict_fin:
max_range = temp_dict_fin['max_range']
if 'error' in temp_dict_fin:
stderr = temp_dict_fin['error']
cont_value_ob = m.ContValue.objects.filter(mean = temp_dict_fin['value'], min_range = min_range, max_range = max_range, stderr = stderr)[0]
if not cont_value_ob:
cont_value_ob = m.ContValue.objects.get_or_create(mean = temp_dict_fin['value'], min_range = min_range, max_range = max_range, stderr = stderr)[0]
metadata_ob = m.MetaData.objects.get_or_create(name='RecTemp', cont_value=cont_value_ob)[0]
update_amd_obj(article, metadata_ob)
aftStatOb = m.ArticleFullTextStat.objects.get_or_create(article_full_text = full_text_ob)[0]
aftStatOb.methods_tag_found = True
aftStatOb.save()
def assign_animal_age(article):
# TODO: find a sentence that mentions recording and temperature or degree celsius
full_text_ob = article.articlefulltext_set.all()[0]
ft = full_text_ob.get_content()
methods_tag = getMethodsTag(ft, article)
if methods_tag is None:
print (article.pmid, article.title, article.journal)
else:
text = re.sub('\s+', ' ', methods_tag.text)
age_dict_list = []
sents = nltk.sent_tokenize(text)
for s in sents:
# print s.encode("iso-8859-15", "replace")
if p_age_re.findall(s):
# print article.pk
# print s.encode("iso-8859-15", "replace")
# print 'Pnumber'
p_iter = re.finditer(ur'P\d', s)
matches = [(match.start(0), match.end(0)) for match in p_iter]
if len(matches) > 0:
p_ind = matches[-1][0]
# p_ind = s.rfind(ur'P\d')
min_sent_ind = 0
max_sent_ind = len(s)
p_close_str = s[np.maximum(min_sent_ind, p_ind-15):np.minimum(max_sent_ind, p_ind+15)]
# print p_close_str
p_close_str = p_close_str.translate(dict((ord(c), u'') for c in string.ascii_letters)).strip()
# print p_close_str
retDict = resolve_data_float(p_close_str)
# print retDict
if 'value' in retDict:
age_dict_list.append(retDict)
elif day_re.findall(s):
# print article.pk
# print s.encode("iso-8859-15", "replace")
# print 'day'
p_iter = re.finditer(ur'\sday', s)
matches = [(match.start(0), match.end(0)) for match in p_iter]
if len(matches) > 0:
p_ind = matches[-1][0]
# p_ind = s.rfind(ur'P\d')
min_sent_ind = 0
max_sent_ind = len(s)
p_close_str = s[np.maximum(min_sent_ind, p_ind-15):np.minimum(max_sent_ind, p_ind+15)]
# print p_close_str
p_close_str = p_close_str.translate(dict((ord(c), u'') for c in string.ascii_letters)).strip()
# print p_close_str
retDict = resolve_data_float(p_close_str)
# print retDict
if 'value' in retDict:
age_dict_list.append(retDict)
if len(age_dict_list) > 0:
# print temp_dict_list
# print age_dict_list
age_dict_fin = validate_age_list(age_dict_list)
# print age_dict_fin
if age_dict_fin:
min_range = None
max_range = None
stderr = None
if 'min_range' in age_dict_fin:
min_range = age_dict_fin['min_range']
if 'max_range' in age_dict_fin:
max_range = age_dict_fin['max_range']
if 'error' in age_dict_fin:
stderr = age_dict_fin['error']
cont_value_ob = m.ContValue.objects.get_or_create(mean = age_dict_fin['value'], min_range = min_range,
max_range = max_range, stderr = stderr)[0]
metadata_ob = m.MetaData.objects.get_or_create(name='AnimalAge', cont_value=cont_value_ob)[0]
update_amd_obj(article, metadata_ob)
aftStatOb = m.ArticleFullTextStat.objects.get_or_create(article_full_text = full_text_ob)[0]
aftStatOb.methods_tag_found = True
aftStatOb.save()
