XML Report Reader

The purpose of this component is reading of standard XML documents with genomics data created by Caris Life Sciences.

It can be used from inside Node.js application API or as an executable CLI.

Installation

npm i @carisls/xmlreport-reader

If you want to use it globally (not only inside application folder) you can install it with -g flag.

npm i -g @carisls/xmlreport-reader

API Usage

const xmlReader = require('@carisls/xmlreport-reader');

const { promises: fs } = require('fs');

(async() => {
  // Get XML file contents
  const fileContents = await fs.readFile('./myfile.xml', 'utf8');

  // Parse XML into Report
  const report = xmlReader(fileContents);

  // Prettify report JSON
  const reportString = JSON.stringify(report, null, 2);

  // Write to console
  console.log(reportString);

})()
  .catch((err) => {
    console.error(err);
  });

CLI Usage

This component can be run as a CLI, too (outside an application).

xmlreport file.xml

If you want to print its output into some file, you can execute

xmlreport file.xml > output.json

Supported elements

Only few elements are currently supported for extraction:

• Cancer-Relevant Biomarkers
• Genomic Signatures
• Immunohistochemistry (IHC)
• Human Leukocyte Antigen (HLA)
• Available Clinical Trials
• References (supporting treatments)