ca.uhn.hl7v2.parser java code examples

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private void myMethod () {
 ArrayList a =new ArrayList<String>()
new ArrayList()
new ArrayList<Object>()
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}

  final String componentKey = componentEntry.getKey();
  final Type component = componentEntry.getValue();
  final String componentValue = HL7_ESCAPING.unescape(component.encode(), HL7_ENCODING);
  if (!StringUtils.isEmpty(componentValue)) {
    attributes.put(componentKey, componentValue);
final String fieldValue = HL7_ESCAPING.unescape(field.encode(), HL7_ENCODING);
if (!StringUtils.isEmpty(fieldValue)) {
  attributes.put(fieldKey, fieldValue);

public HapiField(final Type type) {
  this.value = PipeParser.encode(type, EncodingCharacters.defaultInstance());
  final List<HL7Component> componentList = new ArrayList<>();
  if (type instanceof Composite) {
    final Composite composite = (Composite) type;
    for (final Type component : composite.getComponents()) {
      componentList.add(new HapiField(component));
    }
  }
  final ExtraComponents extra = type.getExtraComponents();
  if (extra != null && extra.numComponents() > 0) {
    final String singleFieldValue;
    if (type instanceof Primitive) {
      singleFieldValue = ((Primitive) type).getValue();
    } else {
      singleFieldValue = this.value;
    }
    componentList.add(new SingleValueField(singleFieldValue));
    for (int i = 0; i < extra.numComponents(); i++) {
      componentList.add(new HapiField(extra.getComponent(i)));
    }
  }
  this.components = Collections.unmodifiableList(componentList);
}

final HapiContext hapiContext = new DefaultHapiContext();
if (!inputVersion.equals("autodetect")) {
  hapiContext.setModelClassFactory(new CanonicalModelClassFactory(inputVersion));
final String hl7Text = new String(buffer, charset);
try {
  final Message message = parser.parse(hl7Text);
  final Map<String, String> attributes = getAttributes(message, useSegmentNames, parseSegmentFields);
  flowFile = session.putAllAttributes(flowFile, attributes);

meta.getFields( data.outputRowMeta, getStepname(), null, null, this, repository, metaStore );
data.parser = new GenericParser();
data.parser.setValidationContext( new NoValidation() );
Message message = data.parser.parse( messageString );
List<HL7Value> values = HL7KettleParser.extractValues( message );

/**
 * @see org.openmrs.hl7.HL7Service#parseHL7String(String)
 */
@Override
public Message parseHL7String(String hl7Message) throws HL7Exception {
  // Any pre-parsing for HL7 messages would go here
  // or a module can use AOP to pre-parse the message
  
  // First, try and parse the message
  Message message;
  try {
    message = parser.parse(hl7Message);
  }
  catch (EncodingNotSupportedException e) {
    throw new HL7Exception("HL7 encoding not supported", e);
  }
  catch (HL7Exception e) {
    throw new HL7Exception("Error parsing message", e);
  }
  
  return message;
}

final HL7Message message;
try {
  final Message hapiMessage = parser.parse(hl7Text);
  message = new HapiMessage(hapiMessage);
} catch (final Exception e) {

Parser parser = new GenericParser();
ValidationContext validationContext = new NoValidation();
parser.setValidationContext( validationContext );
Message msg = parser.parse( message );
Structure structure = msg.get( "MSH" );
String messageType = null;

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test(expected = ApplicationException.class)
public void processMessage_shouldFailOnEmptyConceptAnswers() throws Exception {
  String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080630094800||ORU^R01|kgWdFt0SVwwClOfJm3pe|P|2.5|1||||||||15^AMRS.ELD.FORMID\r"
      + "PID|||3^^^^~d3811480^^^^||John3^Doe^||\r"
      + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20080208|||||||V\r"
      + "ORC|RE||||||||20080208000000|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|1|CWE|5497^CD4, BY FACS^99DCT||^^99DCT|||||||||20080208";
  Message hl7message = parser.parse(hl7string);
  router.processMessage(hl7message);
}

Parser parser = new GenericParser();
ValidationContext validationContext = new NoValidation();
parser.setValidationContext( validationContext );
Message msg = parser.parse( message );
Message ack = msg.generateACK();

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test(expected = ApplicationException.class)
public void processMessage_shouldFailOnEmptyConceptProposals() throws Exception {
  String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080630094800||ORU^R01|kgWdFt0SVwwClOfJm3pe|P|2.5|1||||||||15^AMRS.ELD.FORMID\r"
      + "PID|||3^^^^~d3811480^^^^||John3^Doe^||\r"
      + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20080208|||||||V\r"
      + "ORC|RE||||||||20080208000000|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBR|1|||1284^PROBLEM LIST^99DCT\r"
      + "OBX|1|CWE|6042^PROBLEM ADDED^99DCT||PROPOSED^^99DCT|||||||||20080208";
  Message hl7message = parser.parse(hl7string);
  router.processMessage(hl7message);
}

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test(expected = ApplicationException.class)
public void processMessage_shouldFailIfTheProviderNameTypeCodeIsNotSpecifiedAndIsNotAPersonId() throws Exception {
  int patientId = 2;
  String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ORU^R01|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\r"
      + "PID|||"
      + patientId
      + "^^^^||Hornblower^Horatio^Test||\r"
      + "PV1||O|1^Unknown Location||||Test^Super User (1-8)^^^^^^^&"
      + HL7Constants.PROVIDER_ASSIGNING_AUTH_IDENTIFIER
      + "&^|||||||||||||||||||||||||||||||||||||20080212|||||||V\r"
      + "ORC|RE||||||||20080226102537|1^Super User\r" + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT";
  Message hl7message = parser.parse(hl7string);
  router.processMessage(hl7message);
}

/**
 * @see ORUR01Handler#processNK1(Patient,NK1)
 */
@Test(expected = HL7Exception.class)
public void processNK1_shouldFailIfTheCodingSystemIsNot99REL() throws Exception {
  // process a message with an invalid coding system
  Patient patient = new Patient(3); // the patient that is the focus of
  // this hl7 message
  String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20090728170332||ORU^R01|gu99yBh4loLX2mh9cHaV|P|2.5|1||||||||4^AMRS.ELD.FORMID\r"
      + "PID|||3^^^^||Beren^John^Bondo||\r"
      + "NK1|1|Jones^Jane^Lee^^RN|3A^Parent^ACKFOO||||||||||||F|19751016|||||||||||||||||2^^^L^PI\r"
      + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20090714|||||||V\r"
      + "ORC|RE||||||||20090728165937|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|2|NM|5497^CD4 COUNT^99DCT||123|||||||||20090714\r"
      + "OBR|3|||23^FOOD CONSTRUCT^99DCT\r"
      + "OBX|1|CWE|21^FOOD ASSISTANCE FOR ENTIRE FAMILY^99DCT||22^UNKNOWN^99DCT^2471^UNKNOWN^99NAM|||||||||20090714";
  ORUR01Handler oruHandler = new ORUR01Handler();
  Message hl7message = parser.parse(hl7String);
  ORU_R01 oru = (ORU_R01) hl7message;
  List<NK1> nk1List = oruHandler.getNK1List(oru);
  for (NK1 nk1 : nk1List)
    oruHandler.processNK1(patient, nk1);
}

/**
 * @see ORUR01Handler#processNK1(Patient,NK1)
 */
@Test(expected = HL7Exception.class)
public void processNK1_shouldFailIfTheRelationshipIdentifierIsFormattedImproperly() throws Exception {
  // process a message with an invalid relationship identifier format
  Patient patient = new Patient(3); // the patient that is the focus of
  // this hl7 message
  String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20090728170332||ORU^R01|gu99yBh4loLX2mh9cHaV|P|2.5|1||||||||4^AMRS.ELD.FORMID\r"
      + "PID|||3^^^^||Beren^John^Bondo||\r"
      + "NK1|1|Jones^Jane^Lee^^RN|3C^Parent^99REL||||||||||||F|19751016|||||||||||||||||2^^^L^PI\r"
      + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20090714|||||||V\r"
      + "ORC|RE||||||||20090728165937|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|2|NM|5497^CD4 COUNT^99DCT||123|||||||||20090714\r"
      + "OBR|3|||23^FOOD CONSTRUCT^99DCT\r"
      + "OBX|1|CWE|21^FOOD ASSISTANCE FOR ENTIRE FAMILY^99DCT||22^UNKNOWN^99DCT^2471^UNKNOWN^99NAM|||||||||20090714";
  ORUR01Handler oruHandler = new ORUR01Handler();
  Message hl7message = parser.parse(hl7String);
  ORU_R01 oru = (ORU_R01) hl7message;
  List<NK1> nk1List = oruHandler.getNK1List(oru);
  for (NK1 nk1 : nk1List)
    oruHandler.processNK1(patient, nk1);
}

/**
 * @see ORUR01Handler#processNK1(Patient,NK1)
 */
@Test(expected = HL7Exception.class)
public void processNK1_shouldFailIfTheRelationshipTypeIsNotFound() throws Exception {
  // process a message with a non-existent relationship type
  Patient patient = new Patient(3); // the patient that is the focus of
  // this hl7 message
  String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20090728170332||ORU^R01|gu99yBh4loLX2mh9cHaV|P|2.5|1||||||||4^AMRS.ELD.FORMID\r"
      + "PID|||3^^^^||Beren^John^Bondo||\r"
      + "NK1|1|Jones^Jane^Lee^^RN|3952A^Fifth Cousin Twice Removed^99REL||||||||||||F|19751016|||||||||||||||||2^^^L^PI\r"
      + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20090714|||||||V\r"
      + "ORC|RE||||||||20090728165937|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|2|NM|5497^CD4 COUNT^99DCT||123|||||||||20090714\r"
      + "OBR|3|||23^FOOD CONSTRUCT^99DCT\r"
      + "OBX|1|CWE|21^FOOD ASSISTANCE FOR ENTIRE FAMILY^99DCT||22^UNKNOWN^99DCT^2471^UNKNOWN^99NAM|||||||||20090714";
  ORUR01Handler oruHandler = new ORUR01Handler();
  Message hl7message = parser.parse(hl7String);
  ORU_R01 oru = (ORU_R01) hl7message;
  List<NK1> nk1List = oruHandler.getNK1List(oru);
  for (NK1 nk1 : nk1List)
    oruHandler.processNK1(patient, nk1);
}

/**
 * @see ORUR01Handler#getForm(MSH)
 */
@Test
public void getForm_shouldPassIfReturnValueIsNullWhenUuidAndIdIsNull() throws Exception {
  String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20090728170332||ORU^R01|gu99yBh4loLX2mh9cHaV|P|2.5|1||||||||\r"
      + "PID|||3^^^^||Beren^John^Bondo||\r"
      + "NK1|1|Jones^Jane^Lee^^RN|3A^Parent^99REL||||||||||||F|19751016|||||||||||||||||2^^^L^PI\r"
      + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20090714|||||||V\r"
      + "ORC|RE||||||||20090728165937|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|2|NM|5497^CD4 COUNT^99DCT||123|||||||||20090714\r"
      + "OBR|3|||23^FOOD CONSTRUCT^99DCT\r"
      + "OBX|1|CWE|21^FOOD ASSISTANCE FOR ENTIRE FAMILY^99DCT||22^UNKNOWN^99DCT^2471^UNKNOWN^99NAM|||||||||20090714";
  
  ORUR01Handler oruHandler = new ORUR01Handler();
  Message hl7message = parser.parse(hl7String);
  ORU_R01 oru = (ORU_R01) hl7message;
  ca.uhn.hl7v2.model.v25.segment.MSH msh = oru.getMSH();
  Form form = oruHandler.getForm(msh);
  Assert.assertNull(form);
}

  /**
   * @see ORUR01Handler#getForm(MSH)
   */
  @Test
  public void getForm_shouldPassIfReturnValueIsNotNullWhenUuidOrIdIsNotNull() throws Exception {
    String hl7String = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20090728170332||ORU^R01|gu99yBh4loLX2mh9cHaV|P|2.5|1||||||||16^AMRS.ELD.FORMID\r"
        + "PID|||3^^^^||Beren^John^Bondo||\r"
        + "NK1|1|Jones^Jane^Lee^^RN|3A^Parent^99REL||||||||||||F|19751016|||||||||||||||||2^^^L^PI\r"
        + "PV1||O|1^Unknown||||1^Super User (admin)|||||||||||||||||||||||||||||||||||||20090714|||||||V\r"
        + "ORC|RE||||||||20090728165937|1^Super User\r"
        + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
        + "OBX|2|NM|5497^CD4 COUNT^99DCT||123|||||||||20090714\r"
        + "OBR|3|||23^FOOD CONSTRUCT^99DCT\r"
        + "OBX|1|CWE|21^FOOD ASSISTANCE FOR ENTIRE FAMILY^99DCT||22^UNKNOWN^99DCT^2471^UNKNOWN^99NAM|||||||||20090714";
    
    ORUR01Handler oruHandler = new ORUR01Handler();
    Message hl7message = parser.parse(hl7String);
    ORU_R01 oru = (ORU_R01) hl7message;
    ca.uhn.hl7v2.model.v25.segment.MSH msh = oru.getMSH();
    Form form = oruHandler.getForm(msh);
    Assert.assertNotNull(form);    
    }
}

/**
 * Should create a concept proposal because of the key string in the message
 * 
 * @see ORUR01Handler#processMessage(Message)
 */
@Test
public void processMessage_shouldCreateConceptProposalAndWithObsAlongside() throws Exception {
  
  // remember initial occurrence of proposal's text in the model
  int initialOccurrences = Context.getConceptService().getConceptProposals("ASDFASDFASDF").size();
  
  String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20081006115934||ORU^R01|a1NZBpKqu54QyrWBEUKf|P|2.5|1||||||||3^AMRS.ELD.FORMID\r"
      + "PID|||7^^^^~asdf^^^^||Joe^ ^Smith||\r"
      + "PV1||O|1^Bishop Muge||||1^asdf asdf (5-9)|||||||||||||||||||||||||||||||||||||20081003|||||||V\r"
      + "ORC|RE||||||||20081006115645|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|2|DT|5096^RETURN VISIT DATE^99DCT||20081004|||||||||20081003\r"
      + "OBR|3|||1284^PROBLEM LIST^99DCT\r"
      + "OBX|2|CWE|6042^PROBLEM ADDED^99DCT||PROPOSED^ASDFASDFASDF^99DCT|||||||||20081003";
  Message hl7message = parser.parse(hl7string);
  router.processMessage(hl7message);
  
  //make sure that the proposal was added
  Assert.assertEquals("Processing of the HL7 message did not result in the new proposal being added to the model",
    initialOccurrences + 1, Context.getConceptService().getConceptProposals("ASDFASDFASDF").size());
  
}

/**
 * Should create a concept proposal because of the key string in the message
 * 
 * @see ORUR01Handler#processMessage(Message)
 */
@Test
public void processMessage_shouldCreateBasicConceptProposal() throws Exception {
  
  // remember initial occurrence of proposal's text in the model
  int initialOccurrences = Context.getConceptService().getConceptProposals("PELVIC MASS").size();
  
  String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080924022306||ORU^R01|Z185fTD0YozQ5kvQZD7i|P|2.5|1||||||||3^AMRS.ELD.FORMID\r"
      + "PID|||7^^^^||Joe^S^Mith||\r"
      + "PV1||O|1^Unknown Module 2||||1^Joe (1-1)|||||||||||||||||||||||||||||||||||||20080212|||||||V\r"
      + "ORC|RE||||||||20080219085345|1^Joe\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|18|DT|5096^RETURN VISIT DATE^99DCT||20080506|||||||||20080212\r"
      + "OBR|19|||1284^PROBLEM LIST^99DCT\r"
      + "OBX|1|CWE|6042^PROBLEM ADDED^99DCT||PROPOSED^PELVIC MASS^99DCT|||||||||20080212";
  Message hl7message = parser.parse(hl7string);
  router.processMessage(hl7message);
  
  //make sure that the proposal was added
  Assert.assertEquals("Processing of the HL7 message did not result in the new proposal being added to the model",
    initialOccurrences + 1, Context.getConceptService().getConceptProposals("PELVIC MASS").size());
  
}

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test(expected = ApplicationException.class)
public void processMessage_shouldFailIfQuestionDatatypeIsNeitherBooleanNorNumericNorCoded() throws Exception {
  String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ORU^R01|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\r"
      + "PID|||7^^^^||Collet^Test^Chebaskwony||\r"
      + "PV1||O|1^Unknown Location||||1^Super User (1-8)|||||||||||||||||||||||||||||||||||||20080212|||||||V\r"
      + "ORC|RE||||||||20080226102537|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|2|NM|19^FAVORITE FOOD, NON-CODED^99DCT||1|||||||||20080206";
  Assert.assertEquals("Text", Context.getConceptService().getConcept(19).getDatatype().getName());
  Message hl7message = parser.parse(hl7string);
  router.processMessage(hl7message);
}

/**
 * @see ORUR01Handler#processMessage(Message)
 */
@Test(expected = ApplicationException.class)
public void processMessage_shouldFailIfQuestionDatatypeIsCodedAndABooleanIsNotAValidAnswer() throws Exception {
  GlobalProperty trueConceptGlobalProperty = new GlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_TRUE_CONCEPT, "7",
      "Concept id of the concept defining the TRUE boolean concept");
  GlobalProperty falseConceptGlobalProperty = new GlobalProperty(OpenmrsConstants.GLOBAL_PROPERTY_FALSE_CONCEPT, "8",
      "Concept id of the concept defining the TRUE boolean concept");
  Context.getAdministrationService().saveGlobalProperty(trueConceptGlobalProperty);
  Context.getAdministrationService().saveGlobalProperty(falseConceptGlobalProperty);
  String hl7string = "MSH|^~\\&|FORMENTRY|AMRS.ELD|HL7LISTENER|AMRS.ELD|20080226102656||ORU^R01|JqnfhKKtouEz8kzTk6Zo|P|2.5|1||||||||16^AMRS.ELD.FORMID\r"
      + "PID|||7^^^^||Collet^Test^Chebaskwony||\r"
      + "PV1||O|1^Unknown Location||||1^Super User (1-8)|||||||||||||||||||||||||||||||||||||20080212|||||||V\r"
      + "ORC|RE||||||||20080226102537|1^Super User\r"
      + "OBR|1|||1238^MEDICAL RECORD OBSERVATIONS^99DCT\r"
      + "OBX|2|NM|4^CIVIL STATUS^99DCT||1|||||||||20080206";
  Assert.assertEquals("Coded", Context.getConceptService().getConcept(4).getDatatype().getName());
  Message hl7message = parser.parse(hl7string);
  router.processMessage(hl7message);
}

Most used classes

DefaultModelClassFactory
Default implementation of ModelClassFactory. See packageList() for configuration instructions.
Parser
Parses HL7 message Strings into HL7 Message objects and encodes HL7 Message objects into HL7 message
PipeParser
An implementation of Parser that supports traditionally encoded (ie delimited with characters like |
GenericParser
A Parser that delegates parsing tasks to an underlying PipeParser and DefaultXMLParser as needed. Me
EncodingCharacters
Represents the set of special characters used to encode traditionally encoded HL7 messages.

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