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html_SA_extract.py
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from bs4 import BeautifulSoup
import re
import string
from nltk.corpus import wordnet as wn
def replace(fin_name,srcStr,desStr,fout_name):
fin = open(fin_name, "r")
fout = open(fout_name, "w")
txt = fin.read()
txtout = re.sub(srcStr,desStr, txt)
fout.write(txtout)
fin.close()
fout.close()
filename = input("Input file name : ")
Total_DATA = []
# pretreatment in html file
replace(filename,">\d+\w*[</\w+>]*</a>","></\w+></a>", "temp.html")
html_doc = open("temp.html", encoding = "UTF-8")
# eliminating HTML tags
f = BeautifulSoup(html_doc, 'html.parser')
for i in f(["script","style",'ol','ul','li','table','a','noscript','option']):
i.extract()
for i in f(["div"]):
if i.get('class') == ['citationInfo'] or i.get('class') == ['casRecord'] or i.get('class') == ['casContent'] or i.get('class') == ['casTitle'] or i.get('class') == ['casAuthors'] or i.get('class') == ['casAbstract']:
#print (i.get_text())
i.extract()
for i in f(['sup','sub']):
i.unwrap()
g = f.get_text()
# pretreatment2
g = re.sub("\n","",g)
g = re.sub(" ","",g)
g = re.sub(" "," ",g)
g = re.sub("\u2009"," ",g)
g = re.sub("\u2005"," ",g)
# split in sentences and store in array
sentences = []
sentences = g.split(".")
for i in range(len(sentences)):
sentences[i] += "."
front = re.compile('[^A-Z]\d+.$|\s?Fig.\s?$|\s+\w{1,3}[,.]\s?$|i.e.\s?$')
back = re.compile('^\s?\w?\d+|^g.\s?|^\s?\w+[,.]\s?$|^,')
appended = 0
for i in range(len(sentences)):
value_find = front.search(sentences[i])
temp_sentence = sentences[i]
while value_find != None:
if back.search(sentences[i+1]) != None:
temp_sentence += sentences[i+1]
del sentences[i+1]
sentences.append('\n')
appended += 1
value_find = front.search(temp_sentence)
else:
value_find = None
sentences[i] = temp_sentence
sentences.reverse()
for i in range(appended):
del sentences[0]
sentences.reverse()
# MOF name candidate - MOF criteria : Need to be modified later
Upper = ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z']
Number = ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']
MOF_in_Paper = [];
words = [];
for i in range(len(sentences)):
words = sentences[i].split(' ')
for j in range(len(words)):
# words pretreatment
words[j].replace("-","-")
if len(words[j]) > 2:
if words[j][-1] == ')':
words[j] = words[j][:-1]
if words[j][0] == '(':
words[j] = words[j][1:]
if len(words[j]) > 2:
if words[j][-1] == ',' or words[j][-1] == '.' or words[j][-1] == ';' or words[j][-1] == ':' or words[j][-1] == "\n":
words[j] = words[j][:-1]
if words[j][-1] == ')':
words[j] = words[j][:-1]
if words[j][0] == '(':
words[j] = words[j][1:]
MOF_Crit = 0
MOF_Crit_Number = 0
MOF_Crit_Upper = 0
if words[j].find('-') != -1:
MOF_Crit += 2
if words[j][0] == '-':
MOF_Crit += 1
for k in range(len(Upper)):
if words[j].find(Upper[k]) != -1:
MOF_Crit_Upper += 1
if MOF_Crit_Upper != 0:
MOF_Crit += 1
No_number = 1
for k in range(len(Number)):
if words[j].find(Number[k]) != -1:
MOF_Crit_Number += 1
No_number = 0
if MOF_Crit_Number != 0:
MOF_Crit += 1
if words[j].find('(') * words[j].find(')') >= 0 and words[j].find('(') >= 0:
MOF_Crit += 1
if words[j].find('[') * words[j].find(']') >= 0 and words[j].find('[') >= 0:
MOF_Crit += 1
if words[j].find('MOF') != -1 or words[j].find('PCN') != -1:
MOF_Crit += 1
Linker_words = ["DOBDC","BTC","bdc","CuBT","13X","TO","DBTO","DTO","BTO","Car","bpe","tftpa"]
for k in range(len(Linker_words)):
if words[j].find(Linker_words[k]) != -1:
MOF_Crit += 2
if words[j] == 'AT':
MOF_Crit += 2
if len(words[j]) > 0:
if words[j].find("13X") == -1:
if words[j][0].isdigit() == True or words[j][0] == '+':
MOF_Crit = 0
# Empirically added no MOF words
if words[j].find('MJXp') != -1 or words[j].find('PLATON') != -1:
MOF_Crit = 0
if words[j].find('=') != -1 or words[j].find('=') != -1:
MOF_Crit = 0
if words[j] != '' and words[j][-1] == '-':
MOF_Crit = 0
#if MOF_Crit > 2:
#print (words[j],MOF_Crit)
Prop_noun = 0
if words[j].find('-') != -1:
Prop_noun = 1
tempword = words[j].split('-')
for k in range(len(tempword)):
passlist = ["MIL","POST","NU","rho","sod"]
contin_crit = 0
for l in range(len(passlist)):
if tempword[k] == passlist[l]:
contin_crit = 1
if contin_crit == 1:
continue
#print (tempword[k],len(tempword[k]))
if len(tempword[k]) <= 1:
Prop_noun = 0
if k != 0 and tempword[k].isdigit():
continue
#print (wn.lemmas(tempword[k]))
Atom_word = 0
if len(tempword[k]) == 2 and tempword[k].isalpha() == True and tempword[k][0].isupper() == True and tempword[k][1].islower() == True and wn.lemmas(tempword[k]) != []:
Atom_word = 1
Prop_noun = 0
continue
if len(tempword[k]) > 1 and tempword[k].isdigit() == False and wn.lemmas(tempword[k]) != []:
MOF_Crit = 0
if len(tempword[k]) > 2 and tempword[k].isalpha() == True and tempword[k][0].isupper() == True and tempword[k][1:].islower() == True:
MOF_Crit = 0
break
#if MOF_Crit > 2:
#print (words[j])
if len(words[j]) > 3 and words[j][0].isupper() == True and words[j][1:].islower() == True:
Prop_noun = 1
if Prop_noun == 1:
if No_number == 1 and words[j].find('(') == -1 and words[j].find(')') == -1:
MOF_Crit = 0
if wn.lemmas(words[j]) != [] or words[j] == 'D-R':
MOF_Crit = 0
if len(words[j]) < 3:
MOF_Crit = 0
if MOF_Crit > 2:
if words[j][0].find('(') != -1:
if words[j][-1].find(')') != -1:
words[j] = words[j][1:-1]
if not words[j][0].islower() or words[j][0:3] == 'sod' or words[j][0:3] == 'rho' or words[j][0:3] == 'bio' or words[j].find('agglomerate') != -1: # first letter big
if not words[j][0].isdigit(): # first letter not digit
if len(MOF_in_Paper) != 0:
for l in range(len(MOF_in_Paper)):
if MOF_in_Paper.count(words[j])== 0: #double check
MOF_in_Paper.append(words[j])
else:
MOF_in_Paper.append(words[j])
elif words[j].find('13X') != -1 or Atom_word == 1:
if len(MOF_in_Paper) != 0:
for l in range(len(MOF_in_Paper)):
if MOF_in_Paper.count(words[j])== 0: #double check
MOF_in_Paper.append(words[j])
else:
MOF_in_Paper.append(words[j])
#print (MOF_in_Paper)
# Close file and reopen it to solve BOLD problem
html_doc.close()
html_doc = open("temp.html", encoding = "UTF-8")
#html_doc = open("ref131.html", encoding = "UTF-8")
# eliminating HTML tags - Reference delete
f = BeautifulSoup(html_doc, 'html.parser')
# extracting non usable tags
for i in f(["script","style",'ol','ul','li','table','a','noscript','option']):
i.extract()
for i in f(["div"]):
if i.get('class') == ['citationInfo'] or i.get('class') == ['casRecord'] or i.get('class') == ['casContent'] or i.get('class') == ['casTitle'] or i.get('class') == ['casAuthors'] or i.get('class') == ['casAbstract']:
#print (i.get_text())
i.extract()
#Treating Bold tag MOFs
bold_tag = ['1','1′','2','3','4','5','6','7','7′','8','(1)','(2)','(3)','1a','1b','1c','2a','2b','2c','3a','3b','3c','a','b','c','d','1 a','2 a','2 b','A','B','C','D','1 d','I','II']
bold_tag_candidate = []
bold_MOF = []
for i in f.find_all(['strong','b']):
# set bold MOF tag criteria
bold_tag_Crit = 1
No_number = 1
No_letter = 1
if i.string == None:
continue
i.string = i.string.strip()
for j in range(len(i.string)):
if i.string[j].isdigit() == True:
No_number = 0
if i.string[j].isalpha() == True:
No_letter = 0
if No_number == 1:
if len(i.string) > 2:
bold_tag_Crit = 0
elif No_letter == 1:
bold_tag_Crit = 0
elif No_number == 0 and i.string.isdigit() == True:
if int(i.string) > 1000:
bold_tag_Crit = 0
if i.string[:3] == 'Fig' or i.string[:6] == 'Scheme':
bold_tag_Crit = 0
for j in range(len(MOF_in_Paper)):
if i.string.find(MOF_in_Paper[j]) != -1:
bold_tag_Crit = 0
break
if bold_tag_Crit == 1:
if bold_tag_candidate != []:
for j in range(len(bold_tag_candidate)):
if len(i.string) < 8:
if bold_tag_candidate.count(i.string) == 0:
bold_tag_candidate.append(i.string)
else:
bold_tag_candidate.append(i.string)
#print (bold_tag_candidate)
for i in f.find_all(['strong','b']):
if bold_tag_candidate.count(i.string) == 1:
store = 0
MOF = ''
bold_sentence = i.parent.get_text()
out = 0
start_pos = 0
while out == 0:
bold_index = bold_sentence.find(i.string,start_pos)
pass_crit = 0
if bold_index != -1 and bold_index != 0 and bold_index != len(bold_sentence):
if bold_sentence[bold_index-1].isdigit() or bold_sentence[bold_index-1].isalpha():
pass_crit += 1
if bold_index+len(i.string) <= len(bold_sentence) and bold_sentence[bold_index+len(i.string)].isdigit() or bold_sentence[bold_index+len(i.string)].isalpha():
pass_crit += 1
if pass_crit == 2:
start_pos = bold_index + 1
else:
out = 1
bold_sentence = bold_sentence.split()
#print (bold_sentence)
for k in range(len(bold_sentence)):
bold_index = bold_index - len(bold_sentence[k]) - 1
if bold_index >= 0:
continue
#print (bold_sentence[k])
if store == 0 and bold_sentence[k].find(i.string) != -1:
#print (k)
if k != 0 and k != len(bold_sentence) - 1:
for l in range(len(MOF_in_Paper)):
if bold_sentence[k-1] == 'MOF' or bold_sentence[k-1] == '(MOF':
if bold_sentence[k-2].find(MOF_in_Paper[l]) != -1:
store = 1
MOF = bold_sentence[k-2]
break
if bold_sentence[k-1].find(MOF_in_Paper[l]) != -1:
store = 1
MOF = bold_sentence[k-1]
break
elif bold_sentence[k+1].find(MOF_in_Paper[l]) != -1:
store = 1
MOF = bold_sentence[k+1]
break
elif k == 0:
for l in range(len(MOF_in_Paper)):
if k+1 < len(bold_sentence):
if bold_sentence[k+1].find(MOF_in_Paper[l]) != -1:
store = 1
MOF = bold_sentence[k+1]
break
elif k == len(bold_sentence) - 1:
for l in range(len(MOF_in_Paper)):
if bold_sentence[k-1] == 'MOF' or bold_sentence[k-1] == '(MOF' or bold_sentence[k-1] == 'Compound' or bold_sentence[k-1] == '(Compound':
if bold_sentence[k-2].find(MOF_in_Paper[l]) != -1:
store = 1
MOF = bold_sentence[k-2]
break
if bold_sentence[k-1].find(MOF_in_Paper[l]) != -1:
store = 1
MOF = bold_sentence[k-1]
break
if store == 1:
#print (bold_sentence)
bold_MOF.append(i.string)
bold_MOF.append(MOF)
bold_tag_candidate[bold_tag_candidate.index(i.string)] = ''
#print (bold_MOF)
for i in f.find_all(['strong','b']):
for j in range(int(len(bold_MOF)/2)):
if i.string == bold_MOF[2*j]:
i.string.replace_with(bold_MOF[2*j+1])
# handle table
BET_table = re.compile('SBET|BET|Brunauer\s?[−-]?\W?Emmett\s?[−-]?\W?Teller|Langmuir|Surface\s?area|m2/g|SA\W|m2 g-1', re.I)
BETLang = re.compile('BET|Brunauer\s?[−-]?\W?Emmett\s?[−-]?\W?Teller|Langmuir|SLang|SALm')
BET = re.compile('BET|Brunauer\s?[−-]?\W?Emmett\s?[−-]?\W?Teller')
Lang = re.compile('Langmuir|SLang|SALm')
digit = re.compile('\d+[.,]?\d*|\d+.\d+[·*]10\d+') # digit criteria
tables = f.find_all("table")
for table in tables:
if table.find_all('table') != []:
continue
data = []
if table != None:
table_head = table.thead
head_crit = 0
if table_head != None:
head_crit = 1
rows = table_head.find_all('tr')
rownum = 0
rownow = 0
for row in rows:
rownum += 1
if rownow < rownum:
data.append([])
rownow += 1
cols = row.find_all('th')
colnum = 0
colnow = len(data[rownum - 1])
for col in cols:
#text pretreatment
text = col.text.strip()
text.replace("\n"," ")
text.replace(' ',' ')
text.replace('\n2009',' ')
text.replace(" ","")
colnum += 1
if colnow < colnum:
data[rownum-1].append([])
colnow += 1
while data[rownum-1][colnum-1] != []:
colnum += 1
if colnow < colnum:
data[rownum-1].append([])
colnow += 1
colspannum = 1
#print(col.attrs)
if col.attrs.get('colspan') != None and col.attrs.get('colspan') != '':
colspannum = int(col['colspan'])
rowspannum = 1
if col.attrs.get('rowspan') != None:
rowspannum = int(col['rowspan'])
if rowspannum == 1 and colspannum == 1:
temp = colnum
while data[rownum-1][temp-1] != []:
temp += 1
data[rownum-1][temp-1].append(text)
if rowspannum == 1 and colspannum != 1:
for j in range(colspannum - 1):
data[rownum-1].append([])
colnow += colspannum - 1
for i in range(colspannum):
if data[rownum-1][colnum-1+i] == []:
data[rownum-1][colnum-1+i].append(text)
colnum += colspannum - 1
if rowspannum != 1 and colspannum == 1:
if rownow < rownum + rowspannum-1:
for j in range(rownum + rowspannum - rownow - 1):
data.append([])
rownow += 1
for i in range(rowspannum):
if len(data[rownum+i-1]) < colnum:
for j in range(colnum - len(data[rownum+i-1])):
data[rownum+i-1].append([])
if data[rownum+i-1][colnum-1] == []:
data[rownum+i-1][colnum-1].append(text)
if rowspannum != 1 and colspannum != 1:
if rownow < rownum + rowspannum-1:
for j in range(rownum + rowspannum - rownow - 1):
data.append([])
rownow += 1
for i in range(rowspannum):
if len(data[rownum+i-1]) < colnum + colspannum:
for j in range(colnum + colspannum - len(data[rownum+i-1])):
data[rownum+i-1].append([])
for j in range(colspannum):
if data[rownum+i-1][colnum+j-1] == []:
data[rownum+i-1][colnum+j-1].append(text)
table_body = table.tbody
if table_body != None:
rows = table_body.find_all('tr')
head_row_num = len(data)
if head_row_num == 0:
head_row_num = 1
rownum = len(data)
rownow = len(data)
for row in rows:
rownum += 1
if rownow < rownum:
data.append([])
rownow += 1
cols = row.find_all('td')
colnum = 0
colnow = len(data[rownum - 1])
for col in cols:
#text pretreatment
text = col.text.strip()
text.replace("\n"," ")
text.replace(' ',' ')
text.replace('\u2009',' ')
text.replace(" ","")
colnum += 1
if colnow < colnum:
data[rownum-1].append([])
colnow += 1
while data[rownum-1][colnum-1] != []:
colnum += 1
if colnow < colnum:
data[rownum-1].append([])
colnow += 1
colspannum = 1
if col.attrs.get('colspan') != None and col.attrs.get('colspan') != '':
colspannum = int(col['colspan'])
rowspannum = 1
if col.attrs.get('rowspan') != None:
rowspannum = int(col['rowspan'])
if rowspannum == 1 and colspannum == 1:
temp = colnum
while data[rownum-1][temp-1] != []:
temp += 1;
data[rownum-1][temp-1].append(text)
if rowspannum == 1 and colspannum != 1:
for j in range(colspannum - 1):
data[rownum-1].append([])
colnow += colspannum - 1
for i in range(colspannum):
if data[rownum-1][colnum-1+i] == []:
data[rownum-1][colnum-1+i].append(text)
colnum += colspannum - 1
if rowspannum != 1 and colspannum == 1:
if rownow < rownum + rowspannum-1:
for j in range(rownum + rowspannum - rownow - 1):
data.append([])
rownow += 1
for i in range(rowspannum):
if len(data[rownum+i-1]) < colnum:
for j in range(colnum - len(data[rownum+i-1])):
data[rownum+i-1].append([])
if data[rownum+i-1][colnum-1] == []:
data[rownum+i-1][colnum-1].append(text)
if rowspannum != 1 and colspannum != 1:
if rownow < rownum + rowspannum-1:
for j in range(rownum + rowspannum - rownow - 1):
data.append([])
rownow += 1
for i in range(rowspannum):
if len(data[rownum+i-1]) < colnum + colspannum:
for j in range(colnum + colspannum - len(data[rownum+i-1])):
data[rownum+i-1].append([])
for j in range(colspannum):
if data[rownum+i-1][colnum+j-1] == []:
data[rownum+i-1][colnum+j-1].append(text)
for i in range(len(data)):
for j in range(len(data[i])):
if data[i][j] == []:
data[i][j].append('')
# for i in range(len(data)):
# print(i,data[i])
# print ('\n')
surf_table = 0
surf_column = []
head_type = ''
if data != []:
# if head_row_num != 0:AZZ
# for j in range(head_row_num):
# for i in range(len(data[j])):
# if BET_table.search(data[j][i][0]) != None:
# if BET.search(data[j][i][0]) != None:
# type = 'BET'
# elif Lang.search(data[j][i][0]) != None:
# type = 'Lang'
# else:
# type = '*IDK*'
# head_type = 'top'
# surf_column.append([i,type,head_type])
# surf_table = 1
for i in range(len(data[0])):
surface_finder = ''
if head_row_num == 1:
surface_finder = data[0][i][0]
else:
for j in range(head_row_num):
surface_finder += data[j][i][0]+' '
if BET_table.search(surface_finder) != None:
if BET.search(surface_finder) != None:
type = 'BET'
elif Lang.search(surface_finder) != None:
type = 'Lang'
else:
type = '*IDK*'
head_type = 'top'
surf_column.append([i,type,head_type])
surf_table = 1
for i in range(len(data)):
#print (i,data[i])
if data[i] != [] and BET_table.search(data[i][0][0]) != None:
if BET.search(data[i][0][0]) != None:
type = 'BET'
elif Lang.search(data[i][0][0]) != None:
type = 'Lang'
else:
type = '*IDK*'
head_type = 'left'
surf_column.append([i,type,head_type])
surf_table = 1
#print (surf_column)
if surf_table == 1 and surf_column != []:
print ('<Surface area data in table>\n')
isMOF = 0
if head_type == 'top':
for i in range(len(data)-1):
for j in range(len(MOF_in_Paper)):
if data[i+1][0][0].find(MOF_in_Paper[j]) != -1:
isMOF += 1
MOF_column = 0
if isMOF != 0:
MOF_column = 1
if head_type == 'left':
isMOF = 0
for i in range(head_row_num):
for j in range(len(data[i])-1):
for k in range(len(MOF_in_Paper)):
if data[i][j+1][0].find(MOF_in_Paper[k]) != -1:
isMOF += 1
MOF_column = 1
nowprint = 0
for i in range(len(surf_column)):
if surf_column[i][2] == 'top':
for j in range(len(data) - head_row_num):
if head_row_num == 0 and nowprint == 0:
nowprint = 1
continue
noprint = 0
if digit.search(data[j+head_row_num][surf_column[i][0]][0]) == None:
noprint = 1
if noprint == 0:
MOF_name = ''
MOF_data_in_MOFcol = 0
temp_list = data[head_row_num - 1][surf_column[i][0]][0].split()
for l in range(len(temp_list)):
for m in range(len(MOF_in_Paper)):
if temp_list[l].find(MOF_in_Paper[m]) != -1:
MOF_name = temp_list[l]
MOF_data_in_MOFcol = 1
if MOF_column == 1:
Total_DATA.append([data[j+head_row_num][0][0],surf_column[i][1],data[j+head_row_num][surf_column[i][0]][0],'m2/g'])
print (data[j+head_row_num][0][0],"|",surf_column[i][1],"|",data[j+head_row_num][surf_column[i][0]][0],"|",'m2/g')
elif table.find("caption") != None:
caption = table.find("caption")
caption_text = caption.get_text().split(' ')
for l in range(len(caption_text)):
for m in range(len(MOF_in_Paper)):
if caption_text[l].find(MOF_in_Paper[m]) != -1:
MOF_name = caption_text[l];
MOF_name = MOF_name+'--'+data[head_row_num - 1][0][0]+':'+data[head_row_num+j][0][0]
## state word need to be added
Total_DATA.append([MOF_name, surf_column[i][1],data[j+head_row_num][surf_column[i][0]][0],'m2/g'])
print (MOF_name,"|", surf_column[i][1],"|",data[j+head_row_num][surf_column[i][0]][0],"|",'m2/g')
elif MOF_data_in_MOFcol == 1:
Total_DATA.append([MOF_name, surf_column[i][1],data[j+head_row_num][surf_column[i][0]][0],'m2/g'])
print (MOF_name,"|", surf_column[i][1],"|",data[j+head_row_num][surf_column[i][0]][0],"|",'m2/g')
else:
Total_DATA.append(['*NO_MOF_data*', surf_column[i][1],data[j+head_row_num][surf_column[i][0]][0],'m2/g'])
print ('*NO_MOF_data*',"|", surf_column[i][1],"|",data[j+head_row_num][surf_column[i][0]][0],"|",'m2/g')
elif surf_column[i][2] == 'left':
for j in range(len(data[i]) - 1):
noprint = 0
if digit.search(data[surf_column[i][0]][j+1][0]) == None:
noprint = 1
if noprint == 0:
if MOF_column == 1:
MOF_name = ''
MOF_data_in_MOFcol = 0
temp_list = data[surf_column[i][0]][0][0].split()
for l in range(len(temp_list)):
for m in range(len(MOF_in_Paper)):
if temp_list[l].find(MOF_in_Paper[m]) != -1:
MOF_name = temp_list[l]
MOF_data_in_MOFcol = 1
for k in range(head_row_num):
if MOF_name.find(data[k][j+1][0]) == -1:
MOF_name += data[k][j+1][0]+' '
Total_DATA.append([MOF_name, surf_column[i][1], data[surf_column[i][0]][j+1][0], 'm2/g'])
print (MOF_name,"|", surf_column[i][1],"|", data[surf_column[i][0]][j+1][0],"|", 'm2/g')
elif table.find("caption") != None:
caption = table.find("caption")
caption_text = caption.get_text().split(' ')
for l in range(len(caption_text)):
for m in range(len(MOF_in_Paper)):
if caption_text[l].find(MOF_in_Paper[m]) != -1:
MOF_name = caption_text[l];
## state word need to be added
Total_DATA.append([MOF_name, surf_column[i][1],data[surf_column[i][0]][j+1][0],'m2/g'])
print (MOF_name,"|", surf_column[i][1],"|",data[surf_column[i][0]][j+1][0],"|",'m2/g')
elif MOF_data_in_MOFcol == 1:
Total_DATA.append([MOF_name, surf_column[i][1],data[surf_column[i][0]][j+1][0],'m2/g'])
print (MOF_name,"|", surf_column[i][1],"|",data[surf_column[i][0]][j+1][0],"|",'m2/g')
else:
Total_DATA.append(['*NO_MOF_data*', surf_column[i][1], data[surf_column[i][0]][j+1][0], 'm2/g'])
print ('*NO_MOF_data*',"|", surf_column[i][1],"|", data[surf_column[i][0]][j+1][0],"|", 'm2/g')
for i in f(['table']):
i.extract()
g = f.get_text()
# pretreatment2
g = re.sub("\n","",g)
g = re.sub(" "," ",g)
g = re.sub(" "," ",g)
g = re.sub(" ","",g)
# DIgit format change
exp_form = re.compile('\d+.\d+[·*]10\d+')
# split in sentences and store in array
sentences = []
sentences = g.split(".")
for i in range(len(sentences)):
sentences[i] += "."
appended = 0
for i in range(len(sentences)):
value_find = front.search(sentences[i])
temp_sentence = sentences[i]
while value_find != None:
if back.search(sentences[i+1]) != None:
temp_sentence += sentences[i+1]
del sentences[i+1]
sentences.append('\n')
appended += 1
value_find = front.search(temp_sentence)
else:
value_find = None
sentences[i] = temp_sentence
sentences.reverse()
for i in range(appended):
del sentences[0]
sentences.reverse()
# Experimental / Simulation expectation
exp_crit = 0
sim_crit = 0
# Exp/Sim words
sim = re.compile('simulat', re.I)
exp = re.compile('experiment', re.I)
com = re.compile('computat', re.I)
ff = re.compile('force\s?-?\s?field', re.I)
mc = re.compile('monte\s?-?\s?carlo', re.I)
md = re.compile('molecular\s?-?\s?dynamics', re.I)
for i in range(len(sentences)):
if sim.search(sentences[i]) != None:
sim_crit += 1
if exp.search(sentences[i]) != None:
exp_crit += 1
if com.search(sentences[i]) != None:
sim_crit += 1
if ff.search(sentences[i]) != None:
sim_crit += 1
if mc.search(sentences[i]) != None:
sim_crit += 1
if md.search(sentences[i]) != None:
sim_crit += 1
#if exp_crit > sim_crit:
# print ('This paper is Experiment paper\n')
#elif exp_crit == sim_crit:
# print ('Cannot recongnize Exp/Sim\n')
#else:
# print ('This paper is Simulation paper\n')
# Surface area search
# m2/g finding - m2/g criteria
unit = re.compile('\s?c?m2\s?/\s?g\s?|\s?c?m2\s?\S?\s?g\s?\S?1\s?|\s+c?m2\s?g\s?') # m2/g criteria
range_prob = re.compile('\s?range\s?[-]?\s?of\s\d+\s?\W?\s?\d+|\s?excess\s?of\s?\d+|from\s?\d+\s?to\s?\d+\s?|from\s?\d+|over\s?\d+|\d+\s?~\s?\d+|\d+\s?–\s?\d+|as\s?high\s?as\s?\d+|∼\d+|[<>]\d+|\s?exceeding\s?\d+', re.I)
print ('\n<Surface area data in article>\n')
for i in range(len(sentences)):
data_sentence = unit.findall(sentences[i])
#if data_sentence != []:
#print (sentences[i]) # m2/g sentence
#print ("\n")
unit_index = unit.finditer(sentences[i])
value_list_total = []
m2count = 0
start = 0
end = 0
for match in unit_index:
# Range sentence
start = match.start()
j = 20
while (start - j) <= 0:
j -= 1
temp = sentences[i][start-j:start]
range_sentence = range_prob.search(temp)
if range_sentence != None:
continue
m2count += 1
#print (match.group()) # m2/g
#print (match.span()) # m2/g index in sentence
temptext = str(match.group())
if temptext.find('c') != -1:
unittext = 'cm2/g'
else:
unittext = 'm2/g'
value_count = 0
value_list = []
temp = sentences[i][0:match.start()].split()
#print (temp)
for j in range(len(temp)):
if temp[j][-1:] == '\n':
temp[j] = temp[j][:-1]
temp.reverse()
#print(temp)
value = digit.search(temp[0])
if value != None:
if value.group() == '1':
temp[0] = temp[0][value.end():]
value = digit.search(temp[0])
if value != None:
# Exponental format
exp_check = exp_form.search(temp[0])
store_else = 0
if exp_check != None:
temp0 = exp_check.group()
symb = 0
for k in range(len(temp0)):
if not temp0[k].isdigit():
symb += 1
if symb == 2:
number_part = float(temp0[:k])
exp_part = int(temp0[k+3:])
break
temp[0] = str(number_part * pow(10,exp_part))
store_else = 1
if temp[0].find('±' )== -1 and store_else == 0:
value_list.append(value.group())
elif temp[0].find('±' )== -1 and store_else == 1:
value_list.append(temp[0])
start = 0
counter = 1
none_counter=0
while counter == 1:
for j in range(5):
if start + j + 1 < len(temp):
value = digit.search(temp[start+j+1])
if value != None:
exp_check = exp_form.search(temp[start+j+1])
if exp_check != None:
temp1 = exp_check.group()
symb = 0
for k in range(len(temp1)):
if not temp1[k].isdigit():
symb += 1
if symb == 2:
number_part = float(temp1[:k])
exp_part = int(temp1[k+3:])
break
temp1 = str(number_part * pow(10,exp_part))
prt_thing = temp1
else:
temp1 = value.group()
prt_thing = temp1
not_store = 0
isdigit = 1
for l in range(len(temp1)):
if temp1.find(',') != -1:
temp2 = temp1.split(",")
temp1 = ''
for m in range(len(temp2)):
temp1 += temp2[m]
isdigit = 1
if isdigit == 1 and float(temp1) < float(50.0): # ignore data < 50
not_store = 1
for k in range(len(temp[start+j+1])):
if temp[start+j+1][k].isalpha() == True:
not_store = 1
if not_store == 1:
none_counter += 1
else:
value_list.append(prt_thing)
t = start+j+1
else:
none_counter += 1
else:
counter = 0
t = start
if none_counter == 5:
counter = 0
else:
none_counter = 0
start = t
else:
print ("No_value before_unit_m2/g")
value_list.reverse()
for l in range(len(value_list)):
dontadd = 0
if value_list_total != [] and m2count != 1:
for m in range(len(value_list_total)):
if value_list[l] == value_list_total[m]:
dontadd = 1
value_list[l] = value_list[l].replace(',','')
value_list[l] = value_list[l].replace(' ','')
if float(value_list[l]) < 100:
dontadd = 1
if dontadd == 0:
if value_list[l][-1] == ',':
value_list[l] = value_list[l][:-1]
value_list_total.append(value_list[l])
if data_sentence != []:
#print (value_list_total)
# surface type finding - BET/Langmuir
BET_all = BET.findall(sentences[i])
BET_iter = BET.finditer(sentences[i])
Lang_all = Lang.findall(sentences[i])
Lang_iter = Lang.finditer(sentences[i])
Type = []
Type_index = []
BBLL_type = 0
BBLL = ''
if BET_all == [] and Lang_all == []:
if unit.search(sentences[i-1]) == None:
BET_all = BET.findall(sentences[i-1])
BET_iter = BET.finditer(sentences[i-1])
Lang_all = Lang.findall(sentences[i-1])
Lang_iter = Lang.finditer(sentences[i-1])
if BET_all == [] and Lang_all == []:
Type.append("cannot_find_surface_Type")
elif BET_all != [] and Lang_all == []:
Type.append('BET')
elif BET_all == [] and Lang_all != []:
Type.append('Langmuir')
else:
BBLL_type = 1
sumB = 0
sumL = 0
match_numB = 0
match_numL = 0
for match in BET_iter:
match_numB += 1
sumB += (match.start() + match.end())/2
sumB = sumB/match_numB
for match in Lang_iter:
match_numL += 1
sumL += (match.start() + match.end())/2
sumL = sumL/match_numL
if abs(sumB - sumL) < 30:
BBLL = 'BLBL'
else:
BBLL = 'BBLL'
if sumB < sumL:
Type.append('BET')
Type.append('Langmuir')
else:
Type.append('Langmuir')
Type.append('BET')
elif BET_all != [] and Lang_all == []:
Type.append('BET')
elif BET_all == [] and Lang_all != []:
Type.append('Langmuir')
else:
BBLL_type = 1
sumB = 0
sumL = 0
match_numB = 0
match_numL = 0
for match in BET_iter:
match_numB += 1
sumB += (match.start() + match.end())/2
sumB = sumB/match_numB
for match in Lang_iter:
match_numL += 1
sumL += (match.start() + match.end())/2
sumL = sumL/match_numL
#print (sumB, sumL)
if abs(sumB - sumL) < 30:
BBLL = 'BLBL'
else: