/**
* The contents of this file are subject to the OpenMRS Public License
* Version 1.0 (the "License"); you may not use this file except in
* compliance with the License. You may obtain a copy of the License at
* http://license.openmrs.org
*
* Software distributed under the License is distributed on an "AS IS"
* basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
* License for the specific language governing rights and limitations
* under the License.
*
* Copyright (C) OpenMRS, LLC. All Rights Reserved.
*/
package org.openmrs.hl7.handler;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.util.Calendar;
import java.util.Date;
import java.util.GregorianCalendar;
import java.util.List;
import java.util.Vector;
import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.openmrs.Concept;
import org.openmrs.ConceptName;
import org.openmrs.ConceptProposal;
import org.openmrs.Encounter;
import org.openmrs.Obs;
import org.openmrs.Patient;
import org.openmrs.api.ConceptService;
import org.openmrs.api.EncounterService;
import org.openmrs.api.ObsService;
import org.openmrs.api.context.Context;
import org.openmrs.test.BaseContextSensitiveTest;
import org.openmrs.test.Verifies;
import ca.uhn.hl7v2.app.MessageTypeRouter;
import ca.uhn.hl7v2.model.Message;
import ca.uhn.hl7v2.parser.GenericParser;
/**
* TODO finish testing all methods ORUR01Handler
*/
public class ORUR01HandlerTest extends BaseContextSensitiveTest {
protected static final String ORU_INITIAL_DATA_XML = "org/openmrs/hl7/include/ORUTest-initialData.xml";
// hl7 parser to be used throughout
protected static GenericParser parser = new GenericParser();
private static MessageTypeRouter router = new MessageTypeRouter();
static {
router.registerApplication("ORU", "R01", new ORUR01Handler());
}
/**
* Run this before each unit test in this class. This adds the hl7 specific data to the initial
* and demo data done in the "@Before" method in {@link BaseContextSensitiveTest}.
*
* @throws Exception
*/
@Before
public void runBeforeEachTest() throws Exception {
executeDataSet(ORU_INITIAL_DATA_XML);
}
/**
* @see {@link ORUR01Handler#processMessage(Message)}
*/
@Test
@Verifies(value = "should create encounter and obs from hl7 message", method = "processMessage(Message)")
public void processMessage_shouldCreateEncounterAndObsFromHl7Message() throws Exception {
ObsService obsService = Context.getObsService();
String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ORU^R01|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\rPID|||3^^^^||John3^Doe^||\rPV1||O|1^Unknown Location||||1^Super User (1-8)|||||||||||||||||||||||||||||||||||||20080212|||||||V\rORC|RE||||||||20080226102537|1^Super User\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBX|1|NM|5497^CD4, BY FACS^99DCT||450|||||||||20080206\rOBX|2|DT|5096^RETURN VISIT DATE^99DCT||20080229|||||||||20080212";
Message hl7message = parser.parse(hl7string);
router.processMessage(hl7message);
Patient patient = new Patient(3);
// check for any obs
List<Obs> obsForPatient3 = obsService.getObservationsByPerson(patient);
assertNotNull(obsForPatient3);
assertTrue("There should be some obs created for #3", obsForPatient3.size() > 0);
// check for the return visit date obs
Concept returnVisitDateConcept = new Concept(5096);
Calendar cal = Calendar.getInstance();
cal.set(2008, Calendar.FEBRUARY, 29, 0, 0, 0);
Date returnVisitDate = cal.getTime();
List<Obs> returnVisitDateObsForPatient3 = obsService.getObservationsByPersonAndConcept(patient,
returnVisitDateConcept);
assertEquals("There should be a return visit date", 1, returnVisitDateObsForPatient3.size());
Obs firstObs = (Obs) returnVisitDateObsForPatient3.toArray()[0];
cal.setTime(firstObs.getValueDatetime());
Date firstObsValueDatetime = cal.getTime();
assertEquals("The date should be the 29th", returnVisitDate.toString(), firstObsValueDatetime.toString());
}
/**
* This method checks that obs grouping is happening correctly when processing an ORUR01
*
* @see {@link ORUR01Handler#processMessage(Message)}
*/
@Test
@Verifies(value = "should create obs group for OBRs", method = "processMessage(Message)")
public void processMessage_shouldCreateObsGroupForOBRs() throws Exception {
ObsService obsService = Context.getObsService();
String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226103553||ORU^R01|OD9PWqcD9g0NKn81rvSD|P|2.5|1||||||||66^AMRS.ELD.FORMID\rPID|||3^^^^||John^Doe^||\rPV1||O|1^Unknown Location||||1^Super User (1-8)|||||||||||||||||||||||||||||||||||||20080205|||||||V\rORC|RE||||||||20080226103428|1^Super User\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBX|1|DT|1592^MISSED RETURNED VISIT DATE^99DCT||20080201|||||||||20080205\rOBR|2|||1726^FOLLOW-UP ACTION^99DCT\rOBX|1|CWE|1558^PATIENT CONTACT METHOD^99DCT|1|1555^PHONE^99DCT|||||||||20080205\rOBX|2|NM|1553^NUMBER OF ATTEMPTS^99DCT|1|1|||||||||20080205\rOBX|3|NM|1554^SUCCESSFUL^99DCT|1|1|||||||||20080205";
Message hl7message = parser.parse(hl7string);
router.processMessage(hl7message);
Patient patient = new Patient(3);
Context.clearSession();
// check for any obs
List<Obs> obsForPatient2 = obsService.getObservationsByPerson(patient);
assertNotNull(obsForPatient2);
assertTrue("There should be some obs created for #3", obsForPatient2.size() > 0);
// check for the missed return visit date obs
Concept returnVisitDateConcept = new Concept(1592);
Calendar cal = new GregorianCalendar();
cal.set(2008, Calendar.FEBRUARY, 1, 0, 0, 0);
Date returnVisitDate = cal.getTime();
List<Obs> returnVisitDateObsForPatient2 = obsService.getObservationsByPersonAndConcept(patient,
returnVisitDateConcept);
assertEquals("There should be a return visit date", 1, returnVisitDateObsForPatient2.size());
Obs firstObs = (Obs) returnVisitDateObsForPatient2.toArray()[0];
cal.setTime(firstObs.getValueDatetime());
cal.clear(Calendar.HOUR);
cal.clear(Calendar.MINUTE);
cal.clear(Calendar.SECOND);
cal.clear(Calendar.MILLISECOND);
assertEquals("The date should be the 1st", returnVisitDate.toString(), cal.getTime().toString());
// check for the grouped obs
Concept contactMethod = new Concept(1558);
Concept phoneContact = Context.getConceptService().getConcept(1555);
List<Obs> contactMethodObsForPatient2 = obsService.getObservationsByPersonAndConcept(patient, contactMethod);
assertEquals("There should be a contact method", 1, contactMethodObsForPatient2.size());
Obs firstContactMethodObs = (Obs) contactMethodObsForPatient2.toArray()[0];
assertEquals("The contact method should be phone", phoneContact, firstContactMethodObs.getValueCoded());
// check that there is a group id
Obs obsGroup = firstContactMethodObs.getObsGroup();
assertNotNull("Their should be a grouping obs", obsGroup);
assertNotNull("Their should be an associated encounter", firstContactMethodObs.getEncounter());
// check that the obs that are grouped have the same group id
List<Integer> groupedConceptIds = new Vector<Integer>();
groupedConceptIds.add(1558);
groupedConceptIds.add(1553);
groupedConceptIds.add(1554);
// total obs should be 5
assertEquals(5, obsForPatient2.size());
int groupedObsCount = 0;
for (Obs obs : obsForPatient2) {
if (groupedConceptIds.contains(obs.getConcept().getConceptId())) {
groupedObsCount += 1;
assertEquals("All of the parent groups should match", obsGroup, obs.getObsGroup());
}
}
// the number of obs that were grouped
assertEquals(3, groupedObsCount);
}
/**
* If an hl7 message contains a "visit number" pv1-19 value, then assume its an encounter_id and
* that information in the hl7 message should be appended to that encounter.
*
* @see {@link ORUR01Handler#processMessage(Message)}
*/
@Test
@Verifies(value = "should append to an existing encounter", method = "processMessage(Message)")
public void processMessage_shouldAppendToAnExistingEncounter() throws Exception {
// there should be an encounter with encounter_id == 3 for this test
// to append to
assertNotNull(Context.getEncounterService().getEncounter(3));
String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080902151831||ORU^R01|yow3LEP6bycnLfoPyI31|P|2.5|1||||||||3^AMRS.ELD.FORMID\rPID|||7^^^^||Indakasi^Testarius^Ambote||\rPV1||O|1||||1^Super User (1-8)||||||||||||3|||||||||||||||||||||||||20080831|||||||V\rORC|RE||||||||20080902150000|1^Super User\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBX|1|NM|10^CD4 COUNT^99DCT||250|||||||||20080831";
Message hl7message = parser.parse(hl7string);
router.processMessage(hl7message);
Patient patient = new Patient(7);
Concept question = new Concept(10);
// check that the CD4 count obs in the hl7 message was appended to the
// encounter with encounter_id == 3 and _not_ put into a new encounter
// that has encounter_id == (autoincremented value)
List<Obs> obsForPatient = Context.getObsService().getObservationsByPersonAndConcept(patient, question);
assertEquals(1, obsForPatient.size()); // there should be 1 obs now for this patient
assertEquals(new Encounter(3), obsForPatient.get(0).getEncounter());
}
/**
* Should create a concept proposal because of the key string in the message
*
* @see {@link ORUR01Handler#processMessage(Message)}
*/
@Test
@Verifies(value = "should create basic concept proposal", method = "processMessage(Message)")
public void processMessage_shouldCreateBasicConceptProposal() throws Exception {
// sanity check to make sure we have no concept proposals already
List<ConceptProposal> proposals = Context.getConceptService().getAllConceptProposals(false);
Assert.assertEquals(0, proposals.size());
String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080924022306||ORU^R01|Z185fTD0YozQ5kvQZD7i|P|2.5|1||||||||3^AMRS.ELD.FORMID\rPID|||7^^^^||Joe^S^Mith||\rPV1||O|1^Unknown Module 2||||1^Joe (1-1)|||||||||||||||||||||||||||||||||||||20080212|||||||V\rORC|RE||||||||20080219085345|1^Joe\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBX|18|DT|5096^RETURN VISIT DATE^99DCT||20080506|||||||||20080212\rOBR|19|||5096^PROBLEM LIST^99DCT\rOBX|1|CWE|5096^PROBLEM ADDED^99DCT||PROPOSED^PELVIC MASS^99DCT|||||||||20080212";
Message hl7message = parser.parse(hl7string);
router.processMessage(hl7message);
ConceptProposal proposal = Context.getConceptService().getAllConceptProposals(false).get(0);
assertEquals("PELVIC MASS", proposal.getOriginalText());
}
/**
* Should create a concept proposal because of the key string in the message
*
* @see {@link ORUR01Handler#processMessage(Message)}
*/
@Test
@Verifies(value = "should create concept proposal and with obs alongside", method = "processMessage(Message)")
public void processMessage_shouldCreateConceptProposalAndWithObsAlongside() throws Exception {
// sanity check to make sure we have no concept proposals already
List<ConceptProposal> proposals = Context.getConceptService().getAllConceptProposals(false);
Assert.assertEquals(0, proposals.size());
String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20081006115934||ORU^R01|a1NZBpKqu54QyrWBEUKf|P|2.5|1||||||||3^AMRS.ELD.FORMID\rPID|||7^^^^~asdf^^^^||Joe^ ^Smith||\rPV1||O|1^Bishop Muge||||1^asdf asdf (5-9)|||||||||||||||||||||||||||||||||||||20081003|||||||V\rORC|RE||||||||20081006115645|1^Super User\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBX|1|CWE|5096^PAY CATEGORY^99DCT||5096^PILOT^99DCT|||||||||20081003\rOBX|2|DT|5096^RETURN VISIT DATE^99DCT||20081004|||||||||20081003\rOBR|3|||5096^PROBLEM LIST^99DCT\rOBX|1|CWE|5018^PROBLEM ADDED^99DCT||5096^HUMAN IMMUNODEFICIENCY VIRUS^99DCT|||||||||20081003\rOBX|2|CWE|5089^PROBLEM ADDED^99DCT||PROPOSED^ASDFASDFASDF^99DCT|||||||||20081003";
Message hl7message = parser.parse(hl7string);
router.processMessage(hl7message);
ConceptProposal proposal = Context.getConceptService().getAllConceptProposals(false).get(0);
Assert.assertNotNull(proposal);
assertEquals("ASDFASDFASDF", proposal.getOriginalText());
}
/**
* Tests that a ConceptProposal row can be written by the processor
*
* @see {@link ORUR01Handler#processMessage(Message)}
*/
@Test
@Verifies(value = "should not create problem list observation with concept proposals", method = "processMessage(Message)")
public void processMessage_shouldNotCreateProblemListObservationWithConceptProposals() throws Exception {
ObsService obsService = Context.getObsService();
ConceptService conceptService = Context.getConceptService();
EncounterService encService = Context.getEncounterService();
String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080630094800||ORU^R01|kgWdFt0SVwwClOfJm3pe|P|2.5|1||||||||15^AMRS.ELD.FORMID\rPID|||3^^^^~d3811480^^^^||John3^Doe^||\rPV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20080208|||||||V\rORC|RE||||||||20080208000000|1^Super User\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBR|1|||1284^PROBLEM LIST^99DCT\rOBX|1|CWE|6042^PROBLEM ADDED^99DCT||PROPOSED^SEVERO DOLOR DE CABEZA^99DCT|||||||||20080208";
Message hl7message = parser.parse(hl7String);
router.processMessage(hl7message);
Patient patient = new Patient(3);
// check for any obs
assertEquals("There should not be any obs created for #3", 0, obsService.getObservationsByPerson(patient).size());
// check for a new encounter
assertEquals("There should be 1 new encounter created for #3", 1, encService.getEncountersByPatient(patient).size());
// check for the proposed concept
List<ConceptProposal> proposedConcepts = conceptService.getConceptProposals("SEVERO DOLOR DE CABEZA");
assertEquals("There should be a proposed concept by this name", 1, proposedConcepts.size());
assertEquals(encService.getEncountersByPatient(patient).get(0), proposedConcepts.get(0).getEncounter());
}
/**
* @see {@link ORUR01Handler#processMessage(Message)}
*/
@Test
@Verifies(value = "should create obs valueCodedName", method = "processMessage(Message)")
public void processMessage_shouldCreateObsValueCodedName() throws Exception {
ObsService obsService = Context.getObsService();
Patient patient = new Patient(3); // the patient that is the focus of this hl7 message
Concept concept = new Concept(21); // the question concept for "Food assistance for entire family?"
// sanity check to make sure this obs doesn't exist already
Assert.assertEquals(0, obsService.getObservationsByPersonAndConcept(patient, concept).size());
String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20090728170332||ORU^R01|gu99yBh4loLX2mh9cHaV|P|2.5|1||||||||4^AMRS.ELD.FORMID\rPID|||3^^^^||Beren^John^Bondo||\rPV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20090714|||||||V\rORC|RE||||||||20090728165937|1^Super User\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBX|2|NM|5497^CD4 COUNT^99DCT||123|||||||||20090714\rOBR|3|||23^FOOD CONSTRUCT^99DCT\rOBX|1|CWE|21^FOOD ASSISTANCE FOR ENTIRE FAMILY^99DCT||22^UNKNOWN^99DCT^2471^UNKNOWN^99NAM|||||||||20090714";
Message hl7message = parser.parse(hl7String);
router.processMessage(hl7message);
List<Obs> obss = obsService.getObservationsByPersonAndConcept(patient, concept);
ConceptName name = obss.get(0).getValueCodedName();
Assert.assertNotNull(name);
junit.framework.Assert.assertEquals("The valueCodedName should be 2471", new ConceptName(2471), name);
}
/**
* @see {@link ORUR01Handler#getConcept(String,String)}
*/
@Test
@Verifies(value = "should return a Concept if given local coding system", method = "getConcept(String,String)")
public void getConcept_shouldReturnAConceptIfGivenLocalCodingSystem() throws Exception {
Assert.assertEquals(new Concept(123), new ORUR01Handler().getConcept("123", "99DCT", "xj39bnj4k34nmf"));
}
/**
* @see {@link ORUR01Handler#getConcept(String,String)}
*/
@Test
@Verifies(value = "should return a mapped Concept if given a valid mapping", method = "getConcept(String,String)")
public void getConcept_shouldReturnAMappedConceptIfGivenAValidMapping() throws Exception {
Assert.assertEquals(new Concept(5089), new ORUR01Handler().getConcept("WGT234", "SSTRM", "23498343sdnm3"));
}
/**
* @see {@link ORUR01Handler#getConcept(String,String)}
*/
@Test
@Verifies(value = "should return null if codingSystem not found", method = "getConcept(String,String)")
public void getConcept_shouldReturnNullIfCodingSystemNotFound() throws Exception {
Assert.assertNull(new ORUR01Handler().getConcept("123", "a nonexistent coding system", "n3jn2345g89n4"));
Assert.assertNull(new ORUR01Handler().getConcept("93939434834", "SSTRM", "xcjk23h89gn34k234"));
}
/**
* @see {@link ORUR01Handler#getConcept(String,String)}
*/
@Test
@Verifies(value = "should send message to error queue for empty concept proposals", method = "processMessage(Message)")
public void processMessage__shouldSendMessageToErrorEueueForEmptyConceptProposals()
throws Exception {
String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080630094800||ORU^R01|kgWdFt0SVwwClOfJm3pe|P|2.5|1||||||||15^AMRS.ELD.FORMID\rPID|||3^^^^~d3811480^^^^||John3^Doe^||\rPV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20080208|||||||V\rORC|RE||||||||20080208000000|1^Super User\rOBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\rOBR|1|||1284^PROBLEM LIST^99DCT\rOBX|1|CWE|6042^PROBLEM ADDED^99DCT||PROPOSED^^99DCT|||||||||20080208";
int numberOfErrors = Context.getHL7Service().getAllHL7InErrors().size();
Message hl7message = parser.parse(hl7string);
router.processMessage(hl7message);
Context.getHL7Service().getAllHL7InErrors();
//number or errors in queue should have incremented by 1
Assert.assertEquals(numberOfErrors + 1, Context.getHL7Service().getAllHL7InErrors().size());
}
}