PHC7065 CRITICAL SKILLS IN DATA MANIPULATION FOR POPULATION SCIENCE

Access Web Data

Hui Hu Ph.D.

Department of Epidemiology

College of Public Health and Health Professions & College of Medicine

February 25, 2019

Web Scraping

 

API

 

Lab: Access Web Data

Web Scraping

Client-Network-Server

Internet

HTML, CSS, JavaScript, ...

PHP, MySQL, ...

HTTP, Request, Response, GET, POST, ...

Stack Connections

Transport Control Protocol (TCP):

  • Built on top of IP (Internet Protocol)
     
  • Assume IP may lose some data during transmission, and it will store and retransmit these data
     
  • Provides a reliable pipe 

Stream Sockets / TCP Connections

A stream socket is a type of interprocess communications socket or network socket which provides a connection-oriented, sequenced, and unique flow of data without record boundaries, with well-defined mechanisms for creating and destroying connections and for detecting errors.

Internet

Socket

TCP Port

www.ufl.edu

128.227.9.48

E-mail

23

80

25

Login

Web Server

TCP Port (continued)

Sometimes, the port number is shown (if the server is running on a non-standard port)

Application Protocol

  • What can we do with the TCP socket?
     
  • Application protocols:
    -  a set of rules that all parties follow so that we can predict each other's behavior and not bump into each other
     
  • Examples:
    -  mail
    -  World Wide Web

HTTP

  • The set of rules that allow browsers to retrieve web documents from servers over the internet
     
  • The dominant Application Protocol on the internet
     
  • Invented for the web to retrieve HTML, images, documents, ...
     
  • Extended to be data in addition to documents. E.g. RSS, web services, ...
     
  • Basic flow:
    -  make a connection
    -  request a document
    -  retrieve the document
    -  close the connection

HTTP

http://www.ufl.edu/about

protocol

host

document

Retrieving Data from the Server

  • Each time the user opens a new page, the browser makes a connection to the server and issues a "GET" request - to retrieve the content of the page at the specified URL
     
  • The server returns the HTML document to the browser, which formats and displays the HTML document to the user

Making an HTTP Request

  • Connect to the server, e.g. www.ufl.edu
    -  a "hand shake"
     
  • Request a document
    -  GET http://www.ufl.edu/index.html
     
  • Port 80 is the non-encrypted HTTP port
GET http://www.ufl.edu/index.html

Send HTTP Requests in Python

Python has built-in support for TCP sockets through the socket library

import socket
mysocket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
mysocket.connet( ('www.ufl.edu', 80) )

mysocket.send('GET http://www.ufl.edu/index.html \n\n')

while True:
    data = mysocket.recv(512)
    if ( len(data) < 1 ):
        break
    print data

mysocket.close()

Send HTTP Requests in Python (continued)

We can also use the urllib library, which turns urls to files

import urllib

fhand = urllib.urlopen('http://www.ufl.edu/index.html')

for line in fhand:
    print line.strip()

Web Crawler

Web Scraping

Parsing HTML

  • When a program or script pretends to be a browser to retrieve web pages and to extract information
     
  • Search engines scrape web pages - "web crawling"

Server

Get

HTML

import urllib

fhand = urllib.urlopen('http://www.ufl.edu/index.html')

for line in fhand:
    print line.strip()

Get

HTML

Why Web Scraping?

  • Get data:
    -  e.g. social network data
     
  • Get your own data from some system that has no export capability
     
  • Monitor a site for new information
     
  • Crawl the web to make a search engine

Web Scraping with BeautifulSoup

import urllib
from bs4 import *

html = urllib.urlopen('http://www.ufl.edu/index.html').read()
soup = BeautifulSoup(html,"html5lib")

tags = soup('a')
for tag in tags:
    print tag.get('href',None)

API

Wire Protocol

  • HTML is not really intended for consumption by an application which is interested in data
     
  • We need an agreed way to represent data going between applications and across networks
    -  Wire Protocol
    -  Two common wire format: XML, JSON

Python Dictionary

Java HashMap

Wire Protocol

Serialize

De-Serialize

Web Services

  • Most web applications use services
    -  use services from other applications: credit card charge, etc.
     
  • Services publish the "rules" which must be followed by applications to make use of the service

Application Program Interface

  • Application programming interface (API) is a set of subroutine definitions, protocols, and tools for building application software
     
  • In general terms, it's a set of clearly defined methods of communication between various software components
     
  • Common web service technologies:
    -  SOAP - Simple Object Access Protocol
    -  REST - Representational State Transfer

Google Geocoding API

Security and Rate Limiting

  • The data provided by these APIs is usually valuable
     
  • The data providers might
    -  limit the number of requests per day,
    -  or demand an API "key",
    -  or charge for usage

Increase the limit here: e.g. 1000

Twitter API

  • Documentation
     
  • Twitter uses OAuth to verify authorized requests
     
  • Steps to obtain an access token:
    -  create a new App (need to have a twitter account)
    -  go to "Keys and Access Tokens"
    -  "Create my Access Token"

Lab: Access Web Data

git pull

PHC7065-Spring2019-Lecture6

By Hui Hu

PHC7065-Spring2019-Lecture6

Slides for Lecture 6, Spring 2019, PHC7065 Critical Skills in Data Manipulation for Population Science

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