aculich / Flora-Data-Extraction-and-Cleansing

Flora-Data-Extraction-and-Cleansing

Run this code on:

See also old repo: https://github.com/aculich/extract-flora

How to run

First download the PDF files as flora-book-01.pdf, flora-book-02.pdf, flora-book-03.pdf.

Then extract the csv files and run the cleaning scripts:

python extract-flora-data-from-flora-pdf-files.py
python data-cleansing-of-extracted-flora-data.py
python data-cleansing-of-extracted-flora-data-Syria.py

Installation Notes

Fix error: ModuleNotFoundError: No module named 'frontend'

$ python extract-flora-data-from-flora-pdf-files.py 
Traceback (most recent call last):
  File "extract-flora-data-from-flora-pdf-files.py", line 1, in <module>
    import fitz
  File "/srv/conda/envs/notebook/lib/python3.7/site-packages/fitz/__init__.py", line 1, in <module>
    from frontend import *
ModuleNotFoundError: No module named 'frontend'

The 1.18 version of PyMuPDF does not work, so we need to explicitly downgrade to a previous version.

Requirement already satisfied: PyMuPDF in /srv/conda/envs/notebook/lib/python3.7/site-packages (1.18.19)

See: https://stackoverflow.com/a/63842725/462302

pip install PyMuPDF==1.16.14

So we'll explicitly pin this version of the package in requirements.txt