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Analysis scripts

For running analysis

Install python

We recomand that you activate a virtual environment before.

sh python_install.sh

If you run from analysis-script folder, you might want to set up the PYTHONPATH as below: export PYTHONPATH=$PWD/analysis:$PYTHONPATH

Install docker

sh docker_install.sh

Update .env file

yeah...you have to update it.

# firebase vars
READ_API_URL='https://your_project.cloudfunctions.net/export_json'
READ_TOKEN=''

#docker containers
MYSQL_PORT=3306
PHPMYADMIN_PORT=9000
DOCKER_COVID_MYSQL="docker.covid.mysql"
DOCKER_COVID_ADMIN="docker.covid.phpmyadmin"

# point to your dataset repo
PUBLIC_DATASETS_REPO_RELATIVE_PATH='../datasets'

# other vars
DATABASE_NAME=covid_dev

# your country geocoding file 
GEOCODING_RAW_FILE_URL = "https://raw.githubusercontent.com/ch-covid-19/geo-locations/master/data/mex/MEX_geocoding.csv"

Run docker

Warning, this script is also killing the container berfore restart. So you need to do it once.

sh docker_run.sh

Create the database

  1. Connect to phpmyadmin (http://localhost:9000/db_structure.php)
  2. You have to create a database (default: covid_dev) with the same name as in the .env file.

Run the scripts

Run those scripts only once for initialization:

python analysis/scripts/01_init_db.py
python analysis/scripts/02_upload_geo_data.py

Run those scripts when you want to update database.

To upload new data:

# in case of access to API
python analysis/scripts/03_download_report.py
# in case of not access to API
# then ask for a sample datasets
# that you can load with this script
# the dataset should be put in:
# - backup/documents/<whatever>/<file.json>
python analysis/scripts/90_reload_db_from_json.py

To run analysis:

python analysis/scripts/05_script_analysis.py

To run export to csv:

python analysis/scripts/06_export_csv.py

For backups

Create a backup of NOW

sh docker_db_backup.sh

Relaod a backup

sh docker_db_restore.sh <relative path to the backup>
# example
sh docker_db_restore.sh backups/sql/covid.sql