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CSV Parser

This script parses a csv file of e.g. LOINC codes and descriptions and convert it into a csv file that can be used to import the codes into the MIRACUM MAPPER 2.0. A config file has to be provided in order to tell the parser which columns of the input file have to be mapped to which columns of the output file.

Requirements

  • Python 3.x
  • dependencies from the requirements.txt file installed

Setup

1. Create a Virtual Environment and Install Dependencies

To create and start a virtual environment, open your terminal and run the following command:

python3 -m venv .venv
source .venv/bin/activate

Then install the dependencies:

pip install -r requirements.txt

2. Run the Script

To run the script, execute the following command:

python csv_parser.py -i <path/to/your/input.csv> -c <path/to/your/config.json> -o <path/to/your/output.csv>

Example usage:

python parser.py --input=sample-input.csv --config=sample-config.json --output=sample-output.csv

Configuration

The configuration file is a json file that has to be provided to the script. The keys of the json define the columns of the output file and the values define the columns of the input with a template syntax. An example is given below:

{
  "code": "$LOINC_NUM$",
  "meaning": "Long name: $LONG_COMMON_NAME$ | Short name: $SHORTNAME$"
}

In this example the code column of the output file is mapped to the LOINC_NUM column of the input file. Note that the template syntax is $<column_name>$ for the columns in the input file. The meaning column of the output is handled respectively.

Example usage

Given the following input file sample-input.csv:

LOINC_NUM OTHER_COLUMN LONG_COMMON_NAME SHORTNAME
12345 other Long name 1 Short name 1
67890 other Long name 2 Short name 2

And the configuration file from above, the output file sample-output.csv will look like this:

code meaning
12345 Long name: Long name 1 | Short name: Short name 1
67890 Long name: Long name 2 | Short name: Short name 2