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Covid Act Now Scraping Tools

Creating a development environment for scraping

  1. Install conda (either anaconda or miniconda)
  2. Create conda environment for this project, conda create -n can-scrapers python=3.6
  3. Activate the environment, conda activate can-scrapers
  4. Move your command line or terminal into the can-scrapers directory
  5. Install required packages, pip install -r requirements-dev.txt
  6. (Windows users only) Install required package, conda install fiona
  7. Install development version of package, pip install -e .

Database setup

Our production database is an instance of PostgreSQL on google cloud SQL.

All of our SQL setup and interactions happen through sqlalchemy, which is (mostly) database engine agnostic.

For running integration tests locally there are two options:

  1. Use an in-memory sqlite backend: This is the default setup and will happen automatically for you when you run pytest operations from the local directory (see training/training.org for more info on pytest options).
  2. Use a PostgreSQL server: To use a PostgreSQL server instead, you must set the environment variable CAN_PG_CONN_STR to a proper PostgreSQL connection URI before running pytest. Again see training/training.org for more info

If you would like to work interactively in an IPython session or Jupyter notebook, you can use the function can_tools.models.create_dev_engine to set up an in-memory SQLite instance

Below is a code snippet that sets this up, and then runs the Florida scraper and inserts data into the database

from can_tools.models import create_dev_engine
from can_tools.scrapers import Florida

# setup databsae
engine, Session = create_dev_engine()

scraper = Florida()
df = scraper.normalize(scraper.fetch())

scraper.put(engine, df)

Note that by default the create_dev_engine routine will construct the database in a verbose mode where all SQL commands are echoed to the console. We find that this is helpful while debugging and developing. This can be disabled by passing verbose=False when calling create_dev_engine.

Setting up VS Code

Steps to set up VS code:

  1. Install python and pylance Visual Studio Code extensions
  2. Reload Visual Studio Code
  3. Open can-scrapers directory in Visual Studio Code
  4. Select the can-tools conda environment as the workspace interpreter.

Please do not push any changes made to the .vscode directory. That has some shared settings, but will also be overwritten by the absolute path to the conda environment on your machine. This path is unlikely to match exactly with the path for any other team members

Writing a new scraper

Behind the scenes of every scraper written in can-tools are abstract base classes (ABC). These ABCs define abstract methods fetch, normalize, validate, and put which must be implemented in order to create a scraper.

  • The fetch method should grab the data and return the raw HTML page.
  • The normalize method should transform the raw HTML page into scraped data and return a DataFrame with columns (vintage, dt, location, category, measurement, unit, age, race, ethnicity, sex, value, provider).
  • The validate method should verify the data to ensure that it passes any necessary sanity checks.
  • The put method takes a SQL connection and a DataFrame and then puts the DataFrame into the SQL database.

Most scrapers will not require one to write the validate or put methods because the generic methods should be able to validate the data and dump it into the database

The two core ABCs are DatasetBaseDate and DatasetBaseNoDate. The key difference between these two ABCs is that the get method for DatasetBaseDate expects to receive an argument date to it's get method whereas DatasetBaseNoDate does not expect any arguments to the get method.