美国usan数据库——PDF提取

QQ：231469242 原创

单个PDF内容提取

# -*- coding: utf-8 -*-
"""

io.open() is the preferred, higher-level interface to file I/O. It wraps the OS-level file descriptor in an object that you can use to access the file in a Pythonic manner.

os.open() is just a wrapper for the lower-level POSIX syscall. It takes less symbolic (and more POSIX-y) arguments, and returns the file descriptor (a number) that represents the opened file. It does not return a file object; the returned value will not have read() or write() methods.
"""
import re
from pdfminer.pdfinterp import PDFResourceManager, process_pdf
from pdfminer.converter import TextConverter
from pdfminer.layout import LAParams

# pip3 install pdfminer3k

from io import StringIO
from io import open

#pdf文件名
pdfFilename="avelumab.pdf"
#文件名前缀
frontName="usan/2016/"
#商标文件名
trademark_filename="trademarks.txt"
#赞助商文件名
sponsor_filename="sponsor.txt" 

#读取PDF数据
def readPDF(pdfFile):
    rsrcmgr = PDFResourceManager()
    retstr = StringIO()
    laparams = LAParams()
    device = TextConverter(rsrcmgr, retstr, laparams=laparams)
    process_pdf(rsrcmgr, device, pdfFile)
    device.close()
    content = retstr.getvalue()
    retstr.close()
    return content

#规范PDF数据
def Format(str1):
    list2=[]
    #分割成列表
    list1=str1.split("\n")
    for i in list1:
        #if i=="/n":
        if i=='' or i==' 'or i=='  ':
            continue
        list2.append(i)

    return list2

#提取me_usan，药品名
def Get_me_usan(the_list_data):
    return the_list_data[0]    

#提取me_therapeutic
def Get_me_therapeutic(the_list_data):
    for i in the_list_data:
        if "Treatment of" in i:
            return i

#提取me_chemical1 分子式1
def Get_me_chemical1(the_list_data):
    for i in the_list_data:
        if "1. " in i:
            return i
    return ""

#提取me_chemical2 分子式2
def Get_me_chemical2(the_list_data):
    for i in the_list_data:
        if "2. " in i:
            return i
    return ""   

#匹配分子式
def Re_formula(str1):
    #匹配正在表达式
    re_formula=re.compile(r'C(\d)+H(\d)+')
    mo1=re_formula.search(str1)
    if mo1!=None:
        return True
    return False

#提取me_mo_formula，特征包含碳氢CH元素
def Get_me_mo_formula(the_list_data):
    for i in the_list_data:
        #转换为大写
        i=i.upper()
        value=Re_formula(i)
        if value==True:
            return i

    return ""

#提取分子质量me_mo_weight，如果出现MOLECULAR WEIGHT，且下一个值是数字或浮点数，就提取下一个值
def Get_me_mo_weight(the_list_data):
    for count in range(len(the_list_data)):
        #如果出现MOLECULAR WEIGHT，则提取下一个值
        if 'MOLECULAR WEIGHT' in the_list_data[count]:
            value=the_list_data[count+1]
            if type(eval(value)) == int or type(eval(value)) == float:
                return value
    return ""

#从trademarks.txt搜索数据
def Get_txt_contents(filename):
    file=open(filename)
    content=file.readlines()
    content1=[i.replace("\n","") for i in content]
    return content1

#提取me_trademark，从trademarks.txt搜索数据
def Get_me_trademark(the_list_data):
    for i in the_list_data:
        i=i.strip(" ")
        for k in list_trademarks:
            if k in i:
                return i
    return ""

#提取me_sponsor，从sponsor.txt搜索数据
def Get_me_sponsor(the_list_data):
    for i in the_list_data:
        i=i.strip(" ")
        for k in list_sponsors:
            if k in i:
                return i
    return ""    

#匹配CAS正则表达式
def Re_CAS(str1):
    re_CAS=re.compile(r'(\d)+-(\d)+-(\d)+')
    mo1=re_CAS.search(str1)
    if mo1!=None:
        return True
    return False

#提取CAS
def Get_CAS(the_list_data):
    for i in the_list_data:
        value=Re_CAS(i)
        if value==True:
            return i

    return ""

#匹配WHO正则表达式
def Re_WHO(str1):
    re_WHO=re.compile(r'(\d)+')
    mo1=re_WHO.search(str1)
    if mo1!=None:
        return True
    return False

#提取WHO
def Get_WHO(the_list_data):
    for count in range(len(the_list_data)):
        #如果出现MOLECULAR WEIGHT，则提取下一个值
        try:
            if 'WHO NUMBER' in the_list_data[count]:
                value=the_list_data[count+1]
                if type(eval(value)) == int:
                    return value
        except:
            return ""
    return ""

#匹配UNII正则表达式
def Re_UNII(str1):
    #{10}表示出现10次
    re_UNII=re.compile(r'[A-Za-z0-9]{10}')
    mo1=re_UNII.search(str1)
    if mo1!=None:
        return True
    return False

#提取UNII
def Get_UNII(the_list_data):
    for count in range(len(the_list_data)):
        #如果出现MOLECULAR WEIGHT，则提取下一个值
        if 'UNII' in the_list_data[count]:
            value=the_list_data[count+1]
            if Re_UNII(value)==True:
                return value
    return ""

#获取me_down数据
def Get_me_down(the_list_data):
    name=frontName+pdfFilename
    return name

pdfFile = open(pdfFilename, 'rb')
outputString = readPDF(pdfFile)

list_data=Format(outputString)

me_source=2016

#提取me_usan，药品名
me_usan=Get_me_usan(list_data)
#提取me_therapeutic 治疗疾病
me_therapeutic=Get_me_therapeutic(list_data)
#提取me_therapeutic
me_chemical1=Get_me_chemical1(list_data)

#提取me_chemical2 分子式2
me_chemical2=Get_me_chemical2(list_data)

#提取me_mo_formula，特征包含碳氢CH元素
me_mo_formula=Get_me_mo_formula(list_data)

#提取分子质量me_mo_weight
#me_mo_weight=Get_me_mo_weight(list_data)

#商标名数据库
list_trademarks=Get_txt_contents(trademark_filename)
#提取商标名
me_trademark=Get_me_trademark(list_data)
#赞助商数据库
list_sponsors=Get_txt_contents(sponsor_filename)
#提取赞助商，新公司则找不到
me_sponsor=Get_me_sponsor(list_data)
#提取CAS
me_CAS=Get_CAS(list_data)
#提取WHO
me_WHO=Get_WHO(list_data)
#提取UNII
me_UNII=Get_UNII(list_data)
#获取me_down
me_down=Get_me_down(list_data)
#me_bianma数据默认为空
me_bianma=""
#me_ylbm数据默认为空
me_ylbm=""

me_mo_weight=""

多个PDF内容提取

# -*- coding: utf-8 -*-
"""
Created on Tue Dec 27 11:37:54 2016

批量提取PDF数据到excel内

"""

import re
import os
import pandas,csv
from pdfminer.pdfinterp import PDFResourceManager, process_pdf
from pdfminer.converter import TextConverter
from pdfminer.layout import LAParams

# pip3 install pdfminer3k

from io import StringIO
from io import open

#获取目录内文件名
list_filenames=os.listdir()
#获取所有PDF文件名
list_pdfFilename=[i for i in list_filenames if ".pdf" in i]

#pdf文件名，测试用
#pdfFilename="cenobamate.pdf"

#参数设置
#文件名前缀
frontName="usan/2016/"
#me_sorce字段
me_source=2016
#me_bianma数据默认为空
me_bianma=""
#me_ylbm数据默认为空
me_ylbm=""
me_code=""
me_en=""
#me_mo_weight=""
#疾病诊断文件名
therapeutic_filename="therapeutic.txt"
#商标文件名
trademark_filename="trademarks.txt"
#赞助商文件名
sponsor_filename="sponsor.txt"
#读取PDF数据
def readPDF(pdfFile):
    rsrcmgr = PDFResourceManager()
    retstr = StringIO()
    laparams = LAParams()
    device = TextConverter(rsrcmgr, retstr, laparams=laparams)
    process_pdf(rsrcmgr, device, pdfFile)
    device.close()
    content = retstr.getvalue()
    retstr.close()
    return content

#规范PDF数据
def Format(str1):
    list2=[]
    re_blank=re.compile(r'\s')
    #分割成列表
    list1=str1.split("\n")
    for i in list1:
        m=re_blank.search(i)
        #遇到空格
        if m==None:
            continue
        list2.append(i)

    return list2

#提取me_usan，药品名,并非百分百准确
def Get_me_usan(pdfFilename):
    me_usan=pdfFilename.replace(".pdf","")
    return me_usan    

#提取me_therapeutic
def Get_me_therapeutic(the_list_data):
    for i in the_list_data:
        #小写
        i=i.lower()
        for k in list_therapeutic:
            if k in i:
                return i
    return ""

#提取me_chemical1 分子式1
def Get_me_chemical1(the_list_data):
    for i in the_list_data:
        if "1. " in i:
            return i
    return ""

#提取me_chemical2 分子式2
def Get_me_chemical2(the_list_data):
    for i in the_list_data:
        if "2. " in i:
            return i
    return ""   

#匹配分子式
def Re_formula(str1):
    #匹配正在表达式
    re_formula=re.compile(r'C(\d)+H(\d)+')
    mo1=re_formula.search(str1)
    if mo1!=None:
        return True
    return False

#提取me_mo_formula，特征包含碳氢CH元素
def Get_me_mo_formula(the_list_data):
    for i in the_list_data:
        #转换为大写
        i=i.upper()
        value=Re_formula(i)
        if value==True:
            return i

    return ""

#提取分子质量me_mo_weight，如果出现MOLECULAR WEIGHT，且下一个值是数字或浮点数，就提取下一个值
def Get_me_mo_weight(the_list_data):
    for count in range(len(the_list_data)):
        #如果出现MOLECULAR WEIGHT，则提取下一个值
        if 'MOLECULAR WEIGHT' in the_list_data[count]:
            value=the_list_data[count+1]
            if "kDa" in value:
                return value
            try:
                if type(eval(value)) == int or type(eval(value)) == float:
                    return value
            except:
                return ""
    return ""

#从trademarks.txt搜索数据
def Get_txt_contents(filename):
    file=open(filename)
    content=file.readlines()
    content1=[i.replace("\n","") for i in content]
    #转换为小写
    content2=[i.lower() for i in content1]
    return content2

#提取me_trademark，从trademarks.txt搜索数据
def Get_me_trademark(the_list_data):
    for i in the_list_data:
        i=i.strip(" ")
        for k in list_trademarks:
            if k in i:
                return i
    return ""

#提取me_sponsor，从sponsor.txt搜索数据
def Get_me_sponsor(the_list_data):
    for i in the_list_data:
        i=i.strip(" ")
        for k in list_sponsors:
            if k in i:
                return i
    return ""    

#匹配CAS正则表达式
def Re_CAS(str1):
    re_CAS=re.compile(r'(\d)+-(\d)+-(\d)+')
    mo1=re_CAS.search(str1)
    if mo1!=None:
        return True
    return False

#提取CAS
def Get_CAS(the_list_data):
    for i in the_list_data:
        value=Re_CAS(i)
        if value==True:
            return i

    return ""

#匹配WHO正则表达式
def Re_WHO(str1):
    re_WHO=re.compile(r'(\d)+')
    mo1=re_WHO.search(str1)
    if mo1!=None:
        return True
    return False

#提取WHO
#提取WHO
def Get_WHO(the_list_data):
    for count in range(len(the_list_data)):
        #如果出现MOLECULAR WEIGHT，则提取下一个值
        try:
            if 'WHO NUMBER' in the_list_data[count]:
                value=the_list_data[count+1]
                if type(eval(value)) == int:
                    return value
        except:
            return ""
    return ""

#匹配UNII正则表达式
def Re_UNII(str1):
    #{10}表示出现10次
    re_UNII=re.compile(r'[A-Za-z0-9]{10}')
    mo1=re_UNII.search(str1)
    if mo1!=None:
        return True
    return False

#提取UNII
def Get_UNII(the_list_data):
    for count in range(len(the_list_data)):
        #如果出现MOLECULAR WEIGHT，则提取下一个值
        if 'UNII' in the_list_data[count]:
            value=the_list_data[count+1]
            if Re_UNII(value)==True:
                return value
    return ""

#获取me_down数据
def Get_me_down(pdfFilename):
    name=frontName+pdfFilename
    return name

#获取单个PDF的药品名称，编码，who,unii，分子式等内容
def Get_one_pdf_content(pdfFilename,count):
    list_one_pdf_content=[]
    pdfFile = open(pdfFilename, 'rb')
    outputString = readPDF(pdfFile)
    list_data=Format(outputString)

    #me_uid
    me_uid=count
    #提取me_usan，药品名
    me_usan=Get_me_usan(pdfFilename)
    #提取me_therapeutic 治疗疾病，用字典方法改写
    me_therapeutic=Get_me_therapeutic(list_data)
    #提取me_therapeutic
    me_chemical1=Get_me_chemical1(list_data)
    #提取me_chemical2 分子式2
    me_chemical2=Get_me_chemical2(list_data)
    #提取me_mo_formula，特征包含碳氢CH元素
    me_mo_formula=Get_me_mo_formula(list_data)
    #提取分子质量me_mo_weight,有问题需要改进
    me_mo_weight=Get_me_mo_weight(list_data)
    #提取商标名
    me_trademark=Get_me_trademark(list_data)
    #提取赞助商，新公司则找不到
    me_sponsor=Get_me_sponsor(list_data)
    #提取CAS
    me_CAS=Get_CAS(list_data)
    #提取WHO
    me_WHO=Get_WHO(list_data)
    #提取UNII
    me_UNII=Get_UNII(list_data)
    #获取me_down
    me_down=Get_me_down(pdfFilename)

    #把所有内容添加进去
    list_one_pdf_content.append(me_uid)
    list_one_pdf_content.append(me_source)
    list_one_pdf_content.append(me_usan)
    list_one_pdf_content.append(me_therapeutic)
    list_one_pdf_content.append(me_chemical1)
    list_one_pdf_content.append(me_chemical2)
    list_one_pdf_content.append(me_mo_formula)
    list_one_pdf_content.append(me_mo_weight)
    list_one_pdf_content.append(me_trademark)
    list_one_pdf_content.append(me_sponsor)
    list_one_pdf_content.append(me_code)
    list_one_pdf_content.append(me_CAS)
    list_one_pdf_content.append(me_WHO)
    list_one_pdf_content.append(me_UNII)
    list_one_pdf_content.append(me_en)
    list_one_pdf_content.append(me_down)
    list_one_pdf_content.append(me_bianma)
    list_one_pdf_content.append(me_ylbm)
    return list_one_pdf_content

#获取所有PDF的药品名称，编码，who,unii，分子式等内容
def Get_all_pdf_content(list_pdfFilename):
    #添加首行
    list_all_pdfContent.append(list_firstRow)
    for count in range(len(list_pdfFilename)):
        filename=list_pdfFilename[count]
        try:
            list_one_pdf_content=Get_one_pdf_content(filename,count)
        except:
            list_one_pdf_content=""

        list_all_pdfContent.append(list_one_pdf_content)

    return list_all_pdfContent

#首行信息
list_firstRow=["me_uid","me_source","me_usan","me_therapeutic","me_chemical1","me_chemical2","me_mo_formula","me_mo_weight","me_trademark","me_sponsor",
"me_codename","me_cas","me_who","me_unii","me_en","me_down","me_bianma","me_ylbm"]

#治疗疾病数据库
list_therapeutic=Get_txt_contents(therapeutic_filename)
#商标名数据库
list_trademarks=Get_txt_contents(trademark_filename)
#赞助商数据库
list_sponsors=Get_txt_contents(sponsor_filename)
#获取所有PDF的药品名称，编码，who,unii，分子式等内容
list_all_pdfContent=[]
list_all_pdfContent=Get_all_pdf_content(list_pdfFilename)

csvObj=open("output.csv",'w',newline='')
csvWriter=csv.writer(csvObj)
for rowData in list_all_pdfContent:
    csvWriter.writerow(rowData)
csvObj.close()

需要数据库

自动输出结果