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fits2db: A cli tool to ingest fits files into an sql db

Testing
Package
Docs	Find Here

This is a cli tool to extract table data from a fits file and write it down in a database.

Supported databases

Database	Supported
MySql & MariaDB	YES
DuckDB	In progress
Postgres	under validation

Installation

For installation with pip over the official pypi package index

pip install fits2db

For newer dev verions use the git repository

pip install git+https://github.com/pmodwrc/fits2db.git@main

check if you got the right version with

fits2db --version

To init a config file run

fits2db init

In the config.yml file you now can change the variables needed.

Fill in the database credentials:

database:
  type: mysql
  host: localhost
  user: user
  password: password
  db_name: test_db
  port: 3306

and add some paths for your fits files

fits_files:
  paths:
    - path/to_your_file/2021-07-07_L1a.fits
    - path_to_your_folder

# Delete rows from above listed files from tables which are not listed below
delete_rows_from_missing_tables: True

tables:
    - name: HOUSEKEEPING
      date_column: timestamp # This column will be interpreted as a datetime variable
    - name: OTHER_TABLE # If no table name given it will use the orignal name

Build your database from config file

fits2db build <path_to_config_yaml>

This will create the following tables:

Table	Description
FITS2DB_META	Contain meta information about loaded files
FITS2DB_TABLE_META	Contains info about all loaded tables from the files
HOUSEKEEPING	Contains the data of your fits files tables HOUSEKEEPING merged
HOUSEKEEPING_META	Contains the Column information from the fits files
OTHER_TABLE	Contains the data of your fits files tables HOUSEKEEPING merged
OTHER_TABLE_META	Contains the Column information from the fits files

To add new Files to a existing database use

fits2db update <path_to_config_yaml>

Files which are not yet in the database are added. Already exisitng files are only updated, if their last change time is newer than the already existing one. To force the update of already uploaded files use

fits2db update <path_to_config_yaml> -f