joshuamcginnis/illumina

A collection of utilities for Illumina BaseSpace products.

Illumina BaseSpace API Utils

This repo contains some prototype utilities for various Illumina Basespace product APIs.

Table of Contents

• Utilities
  • FHIR to Clarity Sample XML Translator (f2c)
    • Basic Usage
    • Running the Examples
    • How it works
• Project Setup

FHIR to Clarity Sample XML (f2c)

This is the prototype for a utility that allows translation, translation and connection of raw HL7 data to third-party data sources such as Epic.

Basic Usage

$ python f2c.py --help
Usage: f2c.py [OPTIONS] COMMAND [ARGS]...

  HL7 FHIR to Clarity Payload Utility

Options:
  --help  Show this message and exit.

Commands:
  convert  Translate a FHIR order message to a Clarity LMS /service API...

Save a local FHIR SampleRequest xml and pass it's path to the app.

python f2c.py convert -i path/to/file.xml

Running the Examples

Several example ServiceRequest xml's are available for testing in examples. You can run them like so:

$ python f2c.py convert -i examples/fhir/servicerequest-genetics.xml

<?xml version="1.0" ?>
<smp:samplecreation xmlns:smp="http://genologics.com/ri/sample"
                    xmlns:udf="http://genologics.com/ri/userdefined">
    <name>ABCB4 gene mutation analysis</name>
    <project uri="http://localhost:8080/api/v2/projects/ADM243"/>
    <location>
        <container uri="http://localhost:8080/api/v2/containers/27-100001"/>
        <value>1:1</value>
    </location>
    <date-received>2022-08-23 14:42:46.052753</date-received>
    <udf:field name="request_id">genetics-example-1</udf:field>
    <udf:field name="intent">original-order</udf:field>
    <udf:field name="subject">Patient/example</udf:field>
    <udf:field name="coding_system">http://loinc.org</udf:field>
    <udf:field name="code">49874-1</udf:field>
</smp:samplecreation>

How it Works

Per the most current Hl7 FHIR standards, orders are constructed primarily as <ServiceRequest> objects (with the exception of <MedicationRequest> not currently supported). Previous standards defined an <Order>, but this has since been removed and replaced.

ServiceRequest is a record of a proposal/plan or order for a service to be performed that would result in a Procedure, Observation, DiagnosticReport, ImagingStudy or similar resource.

For now, this project only supports mapping <ServiceRequests> to Clarity Sample creation xml, but is designed to support future mappings between FHIR elements and Clarity LMS xml requests.

FHIR Maps

FHIR maps are python objects which map <ServiceRequest> objects to python objects via xpath.

See: src\fhir_maps\service_request_map.py

These maps are composable and can be used to construct and confine mappings with strict types between FHIR elements to pythonic objects.

Clarity XML Builder

See: src\clarity_xml_builder.py This is the main class for building the sample request xml by mapping the fields defined in FHIR Maps to the Clarity LMS Service creation fields.

Project Setup

Requirements

• Conda (or virtualenv)
• Python 3+

Recreate the python environment and install deps:

$ conda env create -f * environment.yml

Helpful links

• Clarity LMS Sample API documentation
• HL7 FHIR Documentation
• FHIR at EPIC