Illumina BaseSpace API Utils

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

Utilities
- FHIR to Clarity Sample XML Translator (f2c)
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

joshuamcginnis/illumina