healthcare-data-harmonization-lineage

Data Harmonization Lineage

This is not an officially supported Google product.

What is this?

The whistle mapping language is used to map between healtcare schemas such as FHIR and OMOP. This tool reads whistle code and generates a graph representing the lineage of transformations applied to each field.

example whistle code:

x: foo()

def foo() {
  if $Eq(0, 5) {
    y: "true value"
  } else {
    y: "false value"
  }
}

example lineage graph:

Installation

1. Make sure you have a golang development environment set up
2. Download and build the healthcare-data-harmonization
3. Download and build this repository using build.sh. You must provide the path to the healthcare-data-harmonization repository to the build script

Use

Simply run the healthcare-data-harmonization-lineage executable Flags:

• --help
  • display help on flags
• -mapping_file_spec=[path/to/your/mapping.wstl]
  • path and filename of the whistle code you want to generate a graph for
• -dot_out=[path/to/your/dottext.dot]
  • if provided, generates a dot representation of the graph with the given path and file name
• -png_out=[path/to/your/image.png]
  • if provided, generates a png image of the graph with the given path and file name
• -protobuf_out=[path/to/your/protobuf.pb.bin]
  • if provided, generates a serialized protobuf representation of the graph with the given path and file name
• -write_examples=[true|false]
  • if provided, generates images and dot files for the whistle code in examples/. all other flags are ignored if this is activated.