README.md

WHO_pdf_reader

The World Health Organization (WHO) outputs Monthly Risk Assessment Reports in pdf format that describe new instances of the influenza virus at the human-animal interface. This code loops through each report from January, 2017 to the present and extracts the age, gender, onset-date, report-date, and poultry exposure for each reported case of avian influenza strains (H7N9, H5N1). The following csv's are output in the results folder:

• WHO-avian-flu-H5N1-reports_2017-present.csv
• WHO-avian-flu-H7N9-reports_2017-present.csv

This code was written to contribute to a post-doctoral project by Katie Gostic, PhD (University of Chicago) that aims to model the incidence and spread of the avian flu.

• If you are interested in only the csv output, see the results folder for data ranging from January, 2017 - November, 2019 (the most recent report as of posting, January 4, 2020).
• If a more recent report is available that you would like to include or you'd like to run the code on your own:

Instructions for running code:

There are two versions of the main script, (1) read_pdf_url_docker.py, which has absolute filepaths hard-coded to run successfully within the carigostic/who_pdf_reader Docker image, and (2) read_pdf_url.py, which has relative filepaths so the code can run locally.

Using docker

• Download Docker if not already installed
• Download/clone this repository
• Input local absolute path to this repository as indicated in code below and execute the following script in the terminal (Linux):

sudo docker run --rm -v <absolute local path>/who_pdf_reader:/who_pdf_reader carigostic/who_pdf_reader:v1.0 python /who_pdf_reader/read_pdf_url_docker.py 

• View the results folder for csv output

Manually

• Ensure all package dependencies are met (below), including Java version
• Download/clone this repository
• Navigate to the repository in terminal
• Execute the following script in the terminal (Linux):

python read_pdf_url.py` 

• View the results folder for csv output

This code requires Python 3.7 and the following packages:

• re
• pandas
• PyPDF2 == 1.26.0
• tabula-py == 1.4.3
  • tabula requires java version 1.8.0 or greater.
    • Linux/Mac users can check Java version via the terminal (java -version for linux users)
    • Windows users may need to set a path to the Java installation
      • See step 2 of https://aegis4048.github.io/parse-pdf-files-while-retaining-structure-with-tabula-py
• urllib
• bs4 == 0.0.1
• os
• datetime

NOTE: testing has not been confirmed past January, 2017 and oddities/inconsistencies in the wording of the reports may result in errors

To increase the range of data gathered beyond January, 2017, replace the link to the January, 2017 report in line 62 (shown below) with a link to the earliest report you'd like included.

index_2017 = url_list.index('https://www.who.int/influenza/human_animal_interface/Influenza_Summary_IRA_HA_interface_01_16_2017_FINAL.pdf')+1

To include all reports listed on the WHO website, remove the slicing of url_list from the for-loop on line 72.