How to parse HL7 multiple segments(ORC/OBR/OBX) using HAPI Framework.
I am also facing issue related to parsing the multiple lab order and also facing issue related to special character(MSH|^~\&#|) encoding .
MSH|^~\&|NIST Test Lab APP|NIST Lab Facility||NIST EHR Facility|20110531140551-0500||ORU^R01^ORU_R01|NIST-LRI-NG-RN-005.01|T|2.5.1|||AL|NE|||||LRI_Common_Component^^2.16.840.1.113883.9.16^ISO~LRI_NG_Component^^2.16.840.1.113883.9.13^ISO~LRI_RN_Component^^2.16.840.1.113883.9.15^ISO
PID|1||PATID1239^^^NIST MPI^MR||Smirnoff^Peggy^^^^^M||19750401|F||2106-3^White^HL70005^wh^white^L
ORC|RE|ORD448811^NIST EHR|R-511^NIST Lab Filler|||||||||1234567890^Fine^Larry^^^Dr.^^^NIST-AA-1^L^^^NPI
OBR|1|ORD448811^NIST EHR|R-511^NIST Lab Filler|HepABC Panel^Hepatitis A B C Panel^L|||20120628070100|||||||||1234567890^Fine^Larry^^^Dr.^^^NIST-AA-1^L^^^NPI||||||20120629132900-0500|||F
OBX|1|CWE|22314-9^Hepatitis A virus IgM Ab [Presence] in Serum^LN^HAVM^Hepatitis A IgM antibodies (IgM anti-HAV)^L||260385009^Negative (qualifier value)^SCT^NEG^NEGATIVE^L^^^Negative (qualifier value)||Negative|N|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|2|CWE|20575-7^Hepatitis A virus Ab [Presence] in Serum^LN^HAVAB^Hepatitis A antibodies (anti-HAV)^L||260385009^Negative (qualifier value)^SCT^NEG^NEGATIVE^L^^^Negative (qualifier value)||Negative|N|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|3|CWE|16933-4^Hepatitis B virus core Ab [Presence] in Serum^LN^HBVcAB^Hepatitis B core antibodies (anti-HBVc)^L||260385009^Negative (qualifier value)^SCT^NEG^NEGATIVE^L^^^Negative (qualifier value)||Negative|N|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|4|SN|22316-4^Hepatitis B virus core Ab [Units/volume] in Serum^LN^HBcAbQ^Hepatitis B core antibodies (anti-HBVc) Quant^L||^0.40|[IU]/mL^international unit per milliliter^UCUM^IU/ml^^L|<0.50 IU/mL|N|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|5|CWE|22320-6^Hepatitis B virus e Ab [Presence] in Serum^LN^HBVeAB^Hepatitis B e antibodies (anti-HBVe)^L||260385009^Negative (qualifier value)^SCT^NEG^NEGATIVE^L^^^Negative (qualifier value)||Negative|N|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|6|CWE|5195-3^Hepatitis B virus surface Ag [Presence] in Serum^LN^HBVsAG^Hepatitis B surface antigen (HBsAg)^L||260385009^Negative (qualifier value)^SCT^NEG^NEGATIVE^L^^^Negative (qualifier value)||Negative|N|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|7|CWE|22322-2^Hepatitis B virus surface Ab [Presence] in Serum^LN^HBVSAB^Hepatitis B surface antibody (anti-HBVs)^L||260385009^Negative (qualifier value)^SCT^NEG^NEGATIVE^L^^^Negative (qualifier value)||Negative|N|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|8|CWE|16128-1^Hepatitis C virus Ab [Presence] in Serum^LN^HCVAB^Hepatitis C antibody screen (anti-HCV)^L||10828004^Positive (qualifier value)^SCT^POS^POSITIVE^L^^^Positive (qualifier value)||Negative|A|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
OBX|9|SN|48159-8^Hepatitis C virus Ab Signal/Cutoff in Serum or Plasma by Immunoassay^LN^HCVSCO^Hepatitis C antibodies Signal to Cut-off Ratio^L||^10.8|{s_co_ratio}^Signal to cutoff ratio^UCUM^s/co^^L|0.0-0.9 s/co|H|||F|||20120628070100|||||20120628100500||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
NTE|1||Negative: < 0.8; Indeterminate 0.8 - 0.9; Positive: > 0.9. In order to reduce the incidence of a false positive result, the CDC recommends that all s/co ratios between 1.0 and 10.9 be confirmed with additional Verification or PCR testing.
SPM|1|||119364003^Serum specimen (specimen)^SCT^SER^Serum^L|||||||||||||20120628070100
ORC|RE||R-511^NIST Lab Filler|||||||||1234567890^Fine^Larry^^^Dr.^^^NIST-AA-1^L^^^NPI|||||||||||||||||||HepABC Panel^Hepatitis A B C Panel^L
OBR|2||R-511^NIST Lab Filler|11011-4^Hepatitis C virus RNA [Units/volume] (viral load) in Serum or Plasma by Probe and target amplification method^LN^HCVRNA^Hepatitis C RNA PCR^L|||20120628070100||||G|||||1234567890^Fine^Larry^^^Dr.^^^NIST-AA-1^L^^^NPI||||||20120629132900-0500|||F|16128-1&Hepatitis C virus Ab [Presence] in Serum&LN&HCVAB&Hepatitis C antibody screen (anti-HCV)&L|||ORD448811&NIST EHR^R-511&NIST Lab Filler|||||||||||||||||||||HepABC Panel^Hepatitis A B C Panel^L
OBX|1|SN|11011-4^Hepatitis C virus RNA [Units/volume] (viral load) in Serum or Plasma by Probe and target amplification method^LN^HCVRNA^Hepatitis C RNA PCR^L||^7611200|[IU]/mL^international unit per milliliter^UCUM^IU/ml^^L|<43 IU/mL|H|||F|||20120628070100|||||20120629092700||||Princeton Hospital Laboratory^^^^^NIST HCAA-1^XX^^^34D4567890|123 High Street^^Princeton^NJ^08540^USA^O^^34021|^Martin^Steven^M^^Dr.
Code Snippet:
package HAPIHL7Parser.HAPIHL7Parser;
import java.io.FileReader;
import ca.uhn.hl7v2.DefaultHapiContext;
import ca.uhn.hl7v2.HapiContext;
import ca.uhn.hl7v2.model.Message;
import ca.uhn.hl7v2.parser.Parser;
import ca.uhn.hl7v2.util.Hl7InputStreamMessageIterator;
import ca.uhn.hl7v2.util.Terser;
import ca.uhn.hl7v2.validation.impl.NoValidation;
/**
* 40 * Example code for using the {@link Terser} 41 * 42 * @author
* <a href="Sitansu:swainsitansu@gmail.com">Sitansu</a> 43 * @version $Revision:
* 1.3 $ updated on $Date: 2009-08-06 22:43:33 $ by $Author: Sitansu $ 44
*/
public class ExampleUseTerser {
/**
* 49 * A simple example of parsing a message 50 * 51 * @throws HL7Exception
* 52 * @throws EncodingNotSupportedException 53
*/
public static void main(String[] args) throws Exception {
// TODO Auto-generated method stub
FileReader reader = new FileReader("src\\main\\resource\\LRI_5.1-NG-RN_Reflex_Hepatitis_Parent_Child_Message.txt");
// Create an iterator to iterate over all the messages
Hl7InputStreamMessageIterator iter = new Hl7InputStreamMessageIterator(reader);
HapiContext context = new DefaultHapiContext();
context.setValidationContext(new NoValidation());
Parser p = context.getGenericParser();
String msg = null;
while (iter.hasNext()) {
/*
* If we don't already have a connection, create one. 42 * Note that
* unless something goes wrong, it's very common 43 * to keep
* reusing the same connection until we are done 44 * sending
* messages. Many systems keep a connection open 45 * even if a long
* period will pass between messages being 46 * sent. This is good
* practice, as it is much faster than 47 * creating a new
* connection each time. 48
*/
msg = iter.next().toString();
System.out.println("Sent message. Response was " + msg);
}
Message hapiMsg = p.parse(msg);
// Message hapiMsg = p.parse(next);
/*
* 70 * Another way of reading messages is to use a Terser. The terser
* 71 * accepts a particular syntax to retrieve segments. See the API 72
* * documentation for the Terser for more information. 73
*/
Terser terser = new Terser(hapiMsg);
/*
* 77 * Sending Application is in MSH-3-1 (the first component of the
* third 78 * field of the MSH segment) 79
*/
String sendingApplication = terser.get("/.MSH-3");
System.out.println("Sending Application:" + sendingApplication);
String sendingfacility = terser.get("/.MSH-4");
System.out.println("Sending Facility:" + sendingfacility);
String timeofdate = terser.get("/.MSH-7");
System.out.println("Date/time of the message:" + timeofdate);
String messagetype = terser.get("/.MSH-9");
System.out.println("Message Type:" + messagetype);
String messageControlID = terser.get("/.MSH-10");
System.out.println("Message Control ID:" + messageControlID);
String patientIDTypeCode = terser.get("/.PID-3-5");
System.out.println("Patient ID Type Code:" + patientIDTypeCode);
String dateOfBirth = terser.get("/.PID-7");
System.out.println("Date of Birth:" + dateOfBirth);
String placerGroupNumber = terser.get("/.ORC-4-1");
System.out.println("Placer Group Number:" + placerGroupNumber);
String placerOrderNo = terser.get("/.ORC-2-1");
System.out.println("Placer Order Number:" + placerOrderNo);
String fillerOrderNo = terser.get("/.ORC-3-1");
System.out.println("Filler Order Number:" + fillerOrderNo);
String orderProviderID = terser.get("/.ORC-12-1");
System.out.println("Ordering Provider ID:" + orderProviderID);
String orderProviderIDType = terser.get("/.ORC-12-13");
System.out.println("Ordering Provider ID Type:" + orderProviderIDType);
String plcOrderNO = terser.get("/.OBR-2-1");
System.out.println("Placer Order Number:" + plcOrderNO);
String fillrOrdNo = terser.get("/.OBR-3-1");
System.out.println("Filler Order Number:" + fillrOrdNo);
String testCode = terser.get("/.OBR-4-1");
System.out.println("Test Code:" + testCode);
String testDesc = terser.get("/.OBR-4-2");
System.out.println("Test Description:" + testDesc);
String testALTDesc = terser.get("/.OBR-4-9");
System.out.println("Test alternative Description:" + testALTDesc);
String obsDateTime = terser.get("/.OBR-7-1");
System.out.println("Observation Date Time:" + obsDateTime);
String speciActionCode = terser.get("/.OBR-11");
System.out.println("Specimen Action Code:" + speciActionCode);
String relevantClinicInfo = terser.get("/.OBR-13-1");
System.out.println("Relevant Clinical Information:" + relevantClinicInfo);
String relevantClinicInfo2 = terser.get("/.OBR-13-2");
System.out.println("Relevant Clinical Information:" + relevantClinicInfo2);
String resultStatus = terser.get("/.OBR-25");
System.out.println("Result Status:" + resultStatus);
String test = terser.get("/.OBSERVATION(0)/OBX-3-1");
System.out.println("Result Status:" + test);
String test1 = terser.get("/.OBSERVATION(2)/OBX-3-1");
System.out.println("Result Status:" + test1);
String test2 = terser.get("/.OBSERVATION(3)/OBX-3-1");
System.out.println("Result Status:" + test2);
String test3 = terser.get("/.OBSERVATION(4)/OBX-3-1");
System.out.println("Result Status:" + test3);
//terser.getFinder().iterate(, true);
String testNotes = terser.get("/.NTE");
System.out.println("Test Notes:" + testNotes);
String speType = terser.get("/.SPM-4-9");
System.out.println("Specimen Type:" + speType);
String speciRejReason = terser.get("/.SPM-21-9");
System.out.println("Specimen Reject reason:" + speciRejReason);
String specCond = terser.get("/.SPM-24-9");
System.out.println("Specimen condition:" + specCond);
String specCollStartDateTime = terser.get("/.SPM-17-1-1");
System.out.println("Speciment Collection Start Date Time:" + specCollStartDateTime);
String notesCommts = terser.get("/.NTE-3");
System.out.println("Notes and Comments:" + notesCommts);
String obxID = terser.get("/.OBX-3-1");
System.out.println("Observation ID:" + obxID);
String obxText = terser.get("/.OBX-3-2");
System.out.println("Observation Text:" + obxText);
String obxText2 = terser.get("/.OBX-3-9");
System.out.println("Observation Text:" + obxText2);
String obxValue = terser.get("/.OBX-5-1");
System.out.println("Observation Value:" + obxValue);
String obxUnits = terser.get("/.OBX-6-1");
System.out.println("Observation Units:" + obxUnits);
String refRange = terser.get("/.OBX-7");
System.out.println("Reference Range:" + refRange);
String abnormalFlags = terser.get("/.OBX-8");
System.out.println("Abnormal Flags:" + abnormalFlags);
String obXResultStatus = terser.get("/.OBX-11");
System.out.println("Observation Result Status:" + obXResultStatus);
String dateOfObservation = terser.get("/.OBX-14-1");
System.out.println("Date/Time of the Observation:" + dateOfObservation);
String perOrgName = terser.get("/.OBX-23-1");
System.out.println("Performing Organization Name:" + perOrgName);
String perOrgAdd1 = terser.get("/.OBX-24-1");
System.out.println("Performing Organization address Line 1:" + perOrgAdd1);
String perOrgAdd2 = terser.get("/.OBX-24-2");
System.out.println("Performing Organization address Line 2:" + perOrgAdd2);
String perOrgCity = terser.get("/.OBX-24-3");
System.out.println("Performing Organization City:" + perOrgCity);
String perOrgState = terser.get("/.OBX-24-4");
System.out.println("Performing Organization State:" + perOrgState);
String perOrgZipCode = terser.get("/.OBX-24-5");
System.out.println("Performing Organization Zip code:" + perOrgZipCode);
// HIS
/*
* 85 * We can use brackets to get particular repetitions 86
*/
/*
* 108 * MSH|^~\&|||||||ORU^R01|||2.5 109 * OBX|1||ST||This is the value
* for rep 0 110 * OBX|2||ST||This is the value for rep 1 111 *
* OBX|3||ST||This is the value for rep 2 112 * OBX|4||ST||This is the
* value for rep 3 113 * OBX|5||ST||This is the value for rep 4
*/
}
}
You can specify index while get call as below:
String perOrgCity = terser.get("/.OBX1-24-3");
Note the 1 in OBX1 in above code. Indexes zero based. You can simply replace 1 with your loop counter if you want to read multiple of them.
Here is the similar question.