MiringValidator

Semantic Validator for MIRING-compliant HML

National Marrow Donor Program (NMDP)

This is a REST service that validates an HML file according to a MIRING checklist, and returns a XML report specifying any encountered MIRING or HML infractions.

You can import this project into eclipse (Import as a Maven Project), or use the text editor of your choice. I recommend you use java 1.8 and MAVEN to build.

Build MiringValidator.war file using MAVEN:
$ mvn clean install

Deploy /target/MiringValidator.war to your Tomcat 8.0 server, or run within MAVEN:
$ mvn clean install tomcat7:run-war

Once your tomcat server is running, you should find the web interface at:
http://localhost:8080/MiringValidator

MIRING:

MIRING stands for Minimum Information for Reporting Next Generation Sequence Genotyping, and represents a minimum checklist of data to be included in a NGS report.

MIRING is independant of data platform, but this validator is based on HML 1.0.1.

See a MIRING Compliant HML sample at http://schemas.nmdp.org

MIRING: http://biorxiv.org/content/early/2015/02/16/015230
HML: http://biorxiv.org/content/early/2015/02/06/014951

MIRING rules are based on 8 general elements:

MIRING Element 1 - Message Annotation

Message Generator Contact Information & Document Identification

MIRING Element 2 - Reference Context

MIRING Element 3 - Full Genotype

MIRING Element 4 - Consensus Sequence

MIRING Element 5 - Novel Polymorphisms

MIRING Element 6 - Platform Documentation

MIRING Element 7 - Read Processing Documentation

MIRING Element 8 - Primary Data

RULES

The validator further divides these elements into rules. For more information on MIRING elements and a rule ID reference, see http://miring.b12x.org/MoreInfo.html or the local github wiki HERE.

This validator engine is powered by SAX Parser and Probatron4j, an excellent implementation of Schematron

MIRING Validator REST API: Correct Usage

Endpoint

• The Jersey REST endpoint for MIRING validation is: http://localhost:8080/MiringValidator/validator/ValidateMiring
• This is based on:
  • WAR deployed as MiringValidator.war (context path: /MiringValidator)
  • Servlet mapping: /validator/*
  • Jersey resource: @Path("/ValidateMiring")

Form Parameter

• The REST service expects a form parameter named xml (not xml[]).
• The XML payload should be sent as the value of this parameter.

Working curl Command

curl -X POST --data-urlencode "xml=$(cat WebContent/hml/hml_1_0_1_example_miring.xml)" \
  http://localhost:8080/MiringValidator/validator/ValidateMiring

• This will POST the contents of your HML XML file to the correct endpoint and parameter.

Troubleshooting

• 404 errors usually mean the context path, servlet mapping, or resource path is incorrect.
• Always check WAR name, web.xml servlet mapping, and Jersey @Path annotations.

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_Last updated: 2026-01-16 by Jason Brelsford

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