org.mitre.hapifhir

Class MedMorphToCIBMTR

java.lang.Object

org.mitre.hapifhir.MedMorphToCIBMTR

public class MedMorphToCIBMTR
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
MedMorphToCIBMTR(java.lang.String cibmtrUrl)

Method Summary

Modifier and Type	Method and Description
protected org.json.JSONObject	buildMeta(java.lang.String ccn) Helper to construct the resource.meta field with the expected security tag.
protected java.lang.String	checkIfPatientExists(java.lang.String authToken, java.lang.String ccn, java.lang.String crid) Check if a Patient resource for the given CRID already exists on the server.
org.hl7.fhir.r4.model.OperationOutcome	convert(org.hl7.fhir.r4.model.Bundle medmorphReport, org.hl7.fhir.r4.model.MessageHeader messageHeader, java.lang.String authToken) Primary entrypoint into the MedMorph-to-CIBMTR translation process.
protected java.lang.String	getCcn(java.util.List<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> bundleEntries, org.hl7.fhir.r4.model.MessageHeader messageHeader) Extract the CCN for the submitter from MessageHeader.sender.identifier.
protected java.lang.Number	getCrid(java.lang.String authToken, java.lang.String ccn, org.hl7.fhir.r4.model.Patient patient) Register patient with CIBMTR and returns CRID
protected org.json.JSONArray	getObservationEntries(org.apache.http.impl.client.CloseableHttpClient httpClient, java.lang.String authToken, java.lang.String ccn, java.util.List<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> observationEntries, java.lang.String resourceId, boolean isPatientNew) Construct a list of bundle entries for the relevant Observations out of the provided list.
protected int	postBundle(java.lang.String authToken, java.lang.String ccn, java.util.List<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> entries, java.lang.String resourceId, boolean isPatientNew) Convert and POST bundle of observations to the /Bundle endpoint
protected java.lang.String	postPatient(java.lang.String authToken, java.lang.String ccn, java.lang.String crid) POST Patient resource with CRID and return the new resource id.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MedMorphToCIBMTR

public MedMorphToCIBMTR(java.lang.String cibmtrUrl)

Parameters:

cibmtrUrl - Base FHIR endpoint for the target CIBMTR environment.

Method Detail

convert

public org.hl7.fhir.r4.model.OperationOutcome convert(org.hl7.fhir.r4.model.Bundle medmorphReport,
                                                      org.hl7.fhir.r4.model.MessageHeader messageHeader,
                                                      java.lang.String authToken)

Primary entrypoint into the MedMorph-to-CIBMTR translation process. Takes in a MedMorph report bundle and parses out resources to submit to the CIBMTR endpoint, using the submission process defined in the API guidance. 1. Extract the Patient resource and CCN from the request. 2. Obtain a CRID for the given patient info via the /CRID endpoint. 3. Check if a Patient resource for the given CRID already exists. If not, POST the Patient resource to the /Patient endpoint. 4. Check which Observations that are part of the report already exist on the server. POST any that do not as part of a Bundle to the /Bundle endpoint. Returns an OperationOutcome with either error details, if the process was unsuccessful, or basic debugging info if the process was successful.

Parameters:

medmorphReport - MedMorph reporting Bundle

messageHeader - MessageHeader preparsed out of the above Bundle

authToken - Authentication token to passthrough to CIBMTR

Returns:

OperationOutcome with details of success or failure

getCrid

protected java.lang.Number getCrid(java.lang.String authToken,
                                   java.lang.String ccn,
                                   org.hl7.fhir.r4.model.Patient patient)
                            throws java.lang.Exception

Register patient with CIBMTR and returns CRID

Parameters:

authToken - Authentication token

ccn - Submitter CCN

patient - Patient resource

Returns:

CRID

Throws:

java.lang.Exception

checkIfPatientExists

protected java.lang.String checkIfPatientExists(java.lang.String authToken,
                                                java.lang.String ccn,
                                                java.lang.String crid)
                                         throws java.lang.Exception

Check if a Patient resource for the given CRID already exists on the server.

Parameters:

authToken - Authentication token

ccn - Submitter CCN

crid - Patient CRID

Returns:

Patient resource ID, if one already exists, or null if not

Throws:

java.lang.Exception

postPatient

protected java.lang.String postPatient(java.lang.String authToken,
                                       java.lang.String ccn,
                                       java.lang.String crid)
                                throws java.lang.Exception

POST Patient resource with CRID and return the new resource id.

Parameters:

authToken - Authentication token

ccn - Submitter CCN

crid - Patient CRID

Returns:

New Patient resource id, that new Observations will link to

Throws:

java.lang.Exception

postBundle

protected int postBundle(java.lang.String authToken,
                         java.lang.String ccn,
                         java.util.List<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> entries,
                         java.lang.String resourceId,
                         boolean isPatientNew)
                  throws java.lang.Exception

Convert and POST bundle of observations to the /Bundle endpoint

Parameters:

authToken - Authentication token

ccn - Submitter CCN

entries - All entries from the content bundle

resourceId - Patient resource ID

isPatientNew - Whether or not the patient resource is new, if it is then there is no need to dup check on the server

Returns:

the number of Observations that were POSTed, for informational purposes

Throws:

java.lang.Exception

getObservationEntries

protected org.json.JSONArray getObservationEntries(org.apache.http.impl.client.CloseableHttpClient httpClient,
                                                   java.lang.String authToken,
                                                   java.lang.String ccn,
                                                   java.util.List<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> observationEntries,
                                                   java.lang.String resourceId,
                                                   boolean isPatientNew)
                                            throws java.lang.Exception

Construct a list of bundle entries for the relevant Observations out of the provided list. Each observation is first checked to see if it already exists on the server, to avoid duplicates.

Parameters:

httpClient - Client to use to check if resources already exist

authToken - Authentication token to use for dup checking

ccn - Submitter CCN

observationEntries - List of observation entries from the submitted content bundle

resourceId - Patient resource ID to update observation references

isPatientNew - Whether or not the patient already existed on the server - if not, we know none of the Observations already exist either so we can skip the dup check

Returns:

JSONArray of observation entries

Throws:

java.lang.Exception

buildMeta

protected org.json.JSONObject buildMeta(java.lang.String ccn)

Helper to construct the resource.meta field with the expected security tag.

Parameters:

ccn - Submitter CCN

Returns:

JSONObject for resource.meta

getCcn

protected java.lang.String getCcn(java.util.List<org.hl7.fhir.r4.model.Bundle.BundleEntryComponent> bundleEntries,
                                  org.hl7.fhir.r4.model.MessageHeader messageHeader)

Extract the CCN for the submitter from MessageHeader.sender.identifier. The CCN should be stored in an identifier with system "http://cibmtr.org/codesystem/transplant-center"

Parameters:

bundleEntries - List of Bundle.entry

messageHeader - MessageHeader resource that points to the sender

Returns:

CCN string