Spyder

Requirements

Language and framework

• Python 3+
• Scrapy 2.5.0

Main files

• collections.py
  • It is responsable for scraping csv data from form on each collection.
• collections_from_link.py
  • It is responsable for scraping csv and newick data from each collection.

Common files

• generate_file.py
  • It is responsable for create directories and files saving csv and newick data.
• save_csv_file.py
  • It is responsable for create csv files with data from collections.
• save_nwk_file.py
  • It is responsable for create newick file with tree from collections.
• generate_author_id_year.py
  • It is a function responsable for return a tuple with 3 params: author, id and year to create directory name.
• mount_url.py
  • It is a function responsable for return mounted url to scrap data from collection page.
• organisms.py
  • It is a constant to return a tuple of organism and its ids.

Server System Requirements

• Ubuntu Server
• 24GB Memory Ram or 16GB
• 1TB Disk

Used

• Open terminal of your operational system.
• Verify Python version and installation with python --version by terminal.
• If not installed run sudo apt update and sudo apt install python3.8 .
• Verify pip (manager python's libraries) version and installation with pip --version by terminal.
• If not installed run sudo apt install python3-pip .
• Verify git (manager repository) version and installation with git --version by terminal.
• If not installed run sudo apt install git .
• Create a directory for your project
  • mkdir <your directory_name> .
• Into your directory
  • cd <your directory> .
• Before clone git repository you need to setup ssh-key GitHub instructions
• Clone repository to local. git clone https://github.com/lcerdeira/Spyder.git .
• Into to repository cloned.
  • cd Spyder .
• After that run command pip install -r requirements.txt to install required modules.
• Now you stay at main directory. Run scrapy crawl collections on terminal to start webscraping to collecting csv.
• Now you stay at main directory. Run scrapy crawl collections_from_link on terminal to start webscraping to collecting newick.
• The downloaded files will appear on files directory automatically created.

Flow Diagram

API

How to use

After downloaded and generated some files by spider you can see some file by API.

• First you need to go api directory. cd api
• Run command uvicorn main:app
• Now use any browser to see http://localhost:8000/docs. The result must be which appear on GIF.