Modify an IDBac databse, offline

[chasemc]

Note: this will modify your IDBac database. Make sure you have a backup copy before running this

Download the R scripts:
https://gist.github.com/chasemc/25c583becbfff703c1a650b113e3f9d7/archive/c2689a1f10f19960eb2256a51ed91c96f2daa619.zip
and unzip the folder

You ill need R if you don't have it (can be downloaded here https://cran.r-project.org/)

You may have to prepend Rscript to the commands below ( e.g. Rscript path_to_r_script path_to_sqlite_file path_to_csv_file)

The commands to use them are three parts:

1. path_to_r_script 2) path_to_sqlite_file 3) path_to_csv_file

The first script will create a csv file at path_to_csv_file; the second script will read the csv at path_to_csv_file

1. Run the create_metadata_csv.R script first, this will create a new csv file where directed "path_to_csv_file".
   e.g.
   /home/chase/Downloads/create_metadata_csv.R '/home/chase/Downloads/idbac_experiment_file.sqlite' '/home/chase/Downloads/get_table.csv'

2. Modify the new csv to your heart's content Do not add columns. Do not modify anything within the Strain_ID column.

3. Either overwrite the csv, or save as a new csv file

4. Run the second command, final warning: it will overwrite the metadata table of the database
   /home/chase/Downloads/modify_database.R '/home/chase/Downloads/idbac_experiment_file.sqlite' '/home/chase/Downloads/get_table.csv'