NER/PDF/pdf.py

#!pip install pdfreader
import pdfreader
from pdfreader import PDFDocument, SimplePDFViewer
#!pip install bs4
from bs4 import BeautifulSoup
import requests
from NER import cleanText
#!pip install tabula-py
import tabula
import fitz  # PyMuPDF
import os

class PDF():
  def __init__(self, pdf, saveFolder, doi=None):
    self.pdf = pdf
    self.doi = doi
    self.saveFolder = saveFolder

  def openPDFFile(self):
    if "https" in self.pdf:
      name = self.pdf.split("/")[-1]
      name = self.downloadPDF(self.saveFolder)
      if name != "no pdfLink to download":
        fileToOpen = os.path.join(self.saveFolder, name)
      else:
        fileToOpen = self.pdf
    else:
      fileToOpen = self.pdf
    return open(fileToOpen, "rb")

  def downloadPDF(self, saveFolder):
    pdfLink = ''
    if ".pdf" not in self.pdf and "https" not in self.pdf:
      r = requests.get(self.pdf)
      soup = BeautifulSoup(r.content, 'html.parser')
      links = soup.find_all("a")
      for link in links:
        if ".pdf" in link.get("href", ""):
          if self.doi in link.get("href"):
            pdfLink = link.get("href")
            break
    else:
      pdfLink = self.pdf

    if pdfLink != '':
      response = requests.get(pdfLink)
      name = pdfLink.split("/")[-1]
      print("inside download PDF and name and link are: ", pdfLink, name)  
      print("saveFolder is: ", saveFolder)  
      with open(os.path.join(saveFolder, name), 'wb') as pdf:
        print("len of response content: ", len(response.content))  
        pdf.write(response.content)
      print("pdf downloaded")
      return name
    else:
      return "no pdfLink to download"

  def extractText(self):
    try:  
        fileToOpen = self.openPDFFile().name
        try:
          doc = fitz.open(fileToOpen)
          text = ""
          for page in doc:
            text += page.get_text("text") + "\n\n"
          doc.close()
    
          if len(text.strip()) < 100:
            print("Fallback to PDFReader due to weak text extraction.")
            text = self.extractTextWithPDFReader()
          return text
        except Exception as e:
          print("Failed with PyMuPDF, fallback to PDFReader:", e)
          return self.extractTextWithPDFReader()
    except:
        return ""
  def extract_text_excluding_tables(self):
    fileToOpen = self.openPDFFile().name
    text = ""
    try:
        doc = fitz.open(fileToOpen)
        for page in doc:
            blocks = page.get_text("dict")["blocks"]
            
            for block in blocks:
                if block["type"] == 0:  # text block
                    lines = block.get("lines", [])
                    
                    if not lines:
                        continue
                    avg_words_per_line = sum(len(l["spans"]) for l in lines) / len(lines)
                    if avg_words_per_line > 1:  # Heuristic: paragraph-like blocks
                        for line in lines:
                            text += " ".join(span["text"] for span in line["spans"]) + "\n"
        doc.close()
        if len(text.strip()) < 100:
          print("Fallback to PDFReader due to weak text extraction.")
          text = self.extractTextWithPDFReader()
        return text
    except Exception as e:
      print("Failed with PyMuPDF, fallback to PDFReader:", e)
      return self.extractTextWithPDFReader()

  def extractTextWithPDFReader(self):
    jsonPage = {}
    try:
        pdf = self.openPDFFile()
        print("open pdf file")  
        print(pdf)  
        doc = PDFDocument(pdf)
        viewer = SimplePDFViewer(pdf)
        all_pages = [p for p in doc.pages()]
        cl = cleanText.cleanGenText()
        pdfText = ""
        for page in range(1, len(all_pages)):
          viewer.navigate(page)
          viewer.render()
          if str(page) not in jsonPage:
            jsonPage[str(page)] = {}
          text = "".join(viewer.canvas.strings)
          clean, filteredWord = cl.textPreprocessing(text)
          jsonPage[str(page)]["normalText"] = [text]
          jsonPage[str(page)]["cleanText"] = [' '.join(filteredWord)]
          jsonPage[str(page)]["image"] = [viewer.canvas.images]
          jsonPage[str(page)]["form"] = [viewer.canvas.forms]
          jsonPage[str(page)]["content"] = [viewer.canvas.text_content]
          jsonPage[str(page)]["inline_image"] = [viewer.canvas.inline_images]
        pdf.close()
    except:
        jsonPage = {}        
    return self.mergeTextinJson(jsonPage)

  def extractTable(self,pages="all",saveFile=None,outputFormat=None):
    '''pages (str, int, iterable of int, optional) –
      An optional values specifying pages to extract from. It allows str,`int`, iterable of :int. Default: 1
      Examples: '1-2,3', 'all', [1,2]'''
    df = []
    if "https" in self.pdf:
      name = self.pdf.split("/")[-1]
      name = self.downloadPDF(self.saveFolder)
      if name != "no pdfLink to download":
        fileToOpen = self.saveFolder + "/" + name
      else: fileToOpen = self.pdf
    else: fileToOpen = self.pdf
    try:
      df = tabula.read_pdf(fileToOpen, pages=pages)
    # saveFile: "/content/drive/MyDrive/CollectData/NER/PDF/tableS1.csv"
    # outputFormat: "csv"
    #tabula.convert_into(self.pdf, saveFile, output_format=outputFormat, pages=pages)
    except:# ValueError:
      df = []
      print("No tables found in PDF file")
    return df

  def mergeTextinJson(self, jsonPDF):
    try:  
        cl = cleanText.cleanGenText()
        pdfText = ""
        if jsonPDF:  
            for page in jsonPDF:
              if len(jsonPDF[page]["normalText"]) > 0:
                for i in range(len(jsonPDF[page]["normalText"])):
                  text = jsonPDF[page]["normalText"][i]
                  if len(text) > 0:
                    text = cl.removeTabWhiteSpaceNewLine(text)
                    text = cl.removeExtraSpaceBetweenWords(text)
                  jsonPDF[page]["normalText"][i] = text
                  if i - 1 > 0:
                    if jsonPDF[page]["normalText"][i - 1][-1] != ".":
                      pdfText += ". "
                  pdfText += jsonPDF[page]["normalText"][i]
                if len(jsonPDF[page]["normalText"][i]) > 0:
                  if jsonPDF[page]["normalText"][i][-1] != ".":
                    pdfText += "."
                pdfText += "\n\n"
        return pdfText
    except:
        return ""

  def getReference(self):
    pass

  def getSupMaterial(self):
    pass

  def removeHeaders(self):
    pass

  def removeFooters(self):
    pass

  def removeReference(self):
    pass