#import_demo.py
- run_import_demo()
- Calls demographical import class and runs
- Require Dictionary to paths, and path to resources folder, and iram output dir
- Creates json file to store assembly metrics, coverage and depth
#import_demo_helper.py
-
demographics_import() CLASS
- Initialize class
- Requires path to data directory to import both sql db credentials and samples_metrics
- Creates a DF from samples metrics json file
-
get_lims_demographics()
- Imports patient demographical information from HORIZON
- Import PCR results from HORIZON
- Save demographical information to results folder for laster use
-
format_lims_df()
- Formats HORIZON for Influenza DB
-
merge_dfs()
- Umerges both lims_df with sample metrics df
-
database_push()
- Pushes merged DF to Influenza DB
-
setup_db()
- Sets up Influenza DB connection