The dropping of repeats has been causing some trouble for us in production, so
we have investigated further. Within the pipe parser a split method was found
which we believe is the culprit. I pulled it out, created some tests, and have
included a proposed replacement split method. Another alternative using commons
lang was also attempted and included, but it also fails.
See below for code containing splitOriginal, split and splitUseCommons. A set
of test cases are also included.
Hope this helps
Ian
---code---
/*
* To change this template, choose Tools | Templates
* and open the template in the editor.
*/
package hapiexamples;
import java.util.ArrayList;
import java.util.StringTokenizer;
import org.apache.commons.lang.StringUtils;
/**
*
* @author vowlesi
*/
public class ReplaceHapiSplitToCorrectLostTilde {
/**
* Splits the given composite string into an array of components using the
* given delimiter.
*
* @param composite encoded composite string
* @param delim delimiter to split upon
* @return split string
*/
public static String[] splitOriginal(String composite, String delim) {
ArrayList<String> components = new ArrayList<String>();
// defend against evil nulls
if (composite == null) {
composite = "";
}
if (delim == null) {
delim = "";
}
StringTokenizer tok = new StringTokenizer(composite, delim, true);
boolean previousTokenWasDelim = true;
while (tok.hasMoreTokens()) {
String thisTok = tok.nextToken();
if (thisTok.equals(delim)) {
if (previousTokenWasDelim) {
components.add(null);
}
previousTokenWasDelim = true;
} else {
components.add(thisTok);
previousTokenWasDelim = false;
}
}
String[] ret = new String[components.size()];
for (int i = 0; i < components.size(); i++) {
ret[i] = components.get(i);
}
return ret;
}
/**
* Splits the given composite string into an array of components using the
* given delimiter.
*
* @param composite encoded composite string
* @param delim delimiter to split upon
* @return split string
*/
public static String[] split(String composite, String delim) {
// defend against evil nulls
String escapeTheseForSplit = "\\^|.$()*+?[{";
if (composite == null) {
composite = "";
}
if (delim == null) {
String[] ret = new String[]{composite};
return ret;
}
if (escapeTheseForSplit.contains(delim)) {
delim = "\\" + delim;
}
String[] ret = composite.split(delim, -1);
return ret;
}
/**
* Splits the given composite string into an array of components using the
* given delimiter.
*
* @param composite encoded composite string
* @param delim delimiter to split upon
* @return split string
*/
public static String[] splitUseCommons(String composite, String delim) {
// defend against evil nulls
String[] ret = StringUtils.split(composite, delim);
return ret;
}
}
--- tests ---
/*
* To change this license header, choose License Headers in Project Properties.
* To change this template file, choose Tools | Templates
* and open the template in the editor.
*/
package hapiexamples;
import static hapiexamples.ReplaceHapiSplitToCorrectLostTilde.split;
import static hapiexamples.ReplaceHapiSplitToCorrectLostTilde.splitOriginal;
import static hapiexamples.ReplaceHapiSplitToCorrectLostTilde.splitUseCommons;
import org.junit.Test;
import static org.junit.Assert.*;
/**
*
* @author vowlesi
*/
public class ReplaceHapiSplitToCorrectLostTildeTest {
public ReplaceHapiSplitToCorrectLostTildeTest() {
}
/**
* Test of splitOriginal method, of class
* ReplaceHapiSplitToCorrectLostTilde.
*/
@Test
public void testSplitOriginal() {
System.out.println("splitOriginal");
String composite = "Example with trailing repeat delimiters~~~";
String delim = "~";
String[] result = splitOriginal(composite, delim);
assertEquals("With 3 trailing delimiters the array result should have 4
elements", 4, result.length);
}
/**
* Test of proposed replacement split method
* All possible delimiter values within the printable single character
range for HL7 are tested
*/
@Test
public void testSplit() {
System.out.println("split");
for (byte i = 32; i < 127; i++) {
String delim = new String(new byte[] {i});
String composite = "ZZZZ" + delim + delim + delim;
if ("Z".equals(delim)) {
composite = "XXXX" + delim + delim + delim;
}
System.out.println("Counter at " + String.valueOf(i) + " Delimiter
is '" + delim + "'");
String[] result = split(composite, delim);
for (int j = 0; j < result.length; j++) {
System.out.println(j + " " + result[j]);
}
assertEquals("With 3 trailing delimiters the array result should
have 4 elements", 4, result.length);
}
}
/**
* Test of Alternative split using Apache Commons Split version of method
* All possible delimiter values within the printable single character
range for HL7 are tested
*/
@Test
public void testSplitCommonsSplit() {
System.out.println("split");
for (byte i = 32; i < 126; i++) {
String delim = new String(new byte[] {i});
String composite = "ZZZZ" + delim + delim + delim;
if ("Z".equals(delim)) {
composite = "XXXX" + delim + delim + delim;
}
System.out.println("Delimiter is '" + delim + "'");
String[] result = splitUseCommons(composite, delim);
for (int j = 0; j < result.length; j++) {
System.out.println(j + " " + result[j]);
}
assertEquals("With 3 trailing delimiters the array result should
have 4 elements", 4, result.length);
}
}
/**
* Test of proposed replacement split method, of class
* ReplaceHapiSplitToCorrectLostTilde.
*/
@Test
public void testSplitWithNullsPassed() {
System.out.println("split");
String composite = null;
String delim = null;
String[] result = split(composite, delim);
assertEquals("Passing all nulls makes an empty list", 1, result.length);
assertEquals("The one element array has an empty string content", "",
result[0]);
}
/**
* Test of proposed replacement split method, of class
* ReplaceHapiSplitToCorrectLostTilde.
*/
@Test
public void testSplitWithNullPassedAsDelimiter() {
System.out.println("split");
String composite = "Some content";
String delim = null;
String[] result = split(composite, delim);
assertEquals("Passing null delimiter returns a one element array
containing the content", 1, result.length);
assertEquals("The one element array has the original string as
content", composite, result[0]);
}
/**
* Test of proposed replacement split method
* All possible delimiter values within the printable single character
range for HL7 are tested
*/
@Test
public void testSplitWithNullPassedAsCompositeAndAnyDelimiter() {
String composite = null;
for (byte i = 32; i < 126; i++) {
String delim = new String(new byte[] {i});
System.out.println("Delimiter is '" + delim + "'");
String[] result = split(composite, delim);
for (int j = 0; j < result.length; j++) {
System.out.println(j + " '" + result[j] + "'");
}
assertEquals("Passing null content produces a one element array
containing an empty string", 1, result.length);
assertEquals("The one element array has an empty string content",
"", result[0]);
}
}
}
From: Ian Vowles [mailto:ian.vow...@health.qld.gov.au]
Sent: Tuesday, 8 December 2015 7:20 AM
To: hl7api-devel@lists.sourceforge.net
Subject: Re: [HAPI-devel] Parser dropping 1 empty repeat on an OBX-5 each time
you parse
Thanks for your reply James.
I ran the test you provided, and it passed as you expected.
Couple of things.
The OBX-5 provided in the example has 9 repeats. You only had code to test 8.
If you add the line:
assertEquals("", obx.getOBX().getObx5_ObservationValue()[8].encode());
Then the test fails.
Alternatively the assertions could be reduced to:
assertEquals("Count of OBX-5 repeat is 9", 9,
obx.getOBX().getObx5_ObservationValueReps());
Which also fails.
To check if this might be something particular to OBX-5 entries, given their
variable nature I extended the test to include a check on another repeating
field by adding 3 repeat characters to the end of the PID-3 list (making 4
repeats)
+ "PID|1||10011682^^^CL_MRN
Pool^^CD:237968946~~~|60683166^^^DONOTSEND^^CD:237968946|CLABTEST^ONE||19500101120000|F||C|34605
W 12 MILE RD^^FARM
MILLS^MN^48331-3263^CD:309221^CD:756^^CD:637908|CD:637908|(248)489-6000^CD:170||CD:151|M|CD:3391461|606831661088^^^DONOTSEND^FIN
NBR^CD:237968946||||CD:654655774|||0|||CD:654897458\r"
and added another assertion:
assertEquals("Count of PID-3 repeat is 4", 4, ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getPATIENT().getPID().getPid3_PatientIdentifierListReps());
This also fails.
Any thoughts on what is going on?
Thanks
Ian
From: James Agnew [mailto:jamesag...@gmail.com]
Sent: Monday, 7 December 2015 11:13 PM
To: Ian Vowles
Cc: hl7api-devel@lists.sourceforge.net
Subject: Re: [HAPI-devel] Parser dropping 1 empty repeat on an OBX-5 each time
you parse
Hi Ian,
I turned this into a unit test, and it seems to give me the expected results:
String msg =
"MSH|^~\\&|HNAM|CL|CL_RADNET|CL|20110628095233||ORU^R01|Q2301030099T1904270849|P|2.4\r"
+ "PID|1||10011682^^^CL_MRN
Pool^^CD:237968946|60683166^^^DONOTSEND^^CD:237968946|CLABTEST^ONE||19500101120000|F||C|34605
W 12 MILE RD^^FARM
MILLS^MN^48331-3263^CD:309221^CD:756^^CD:637908|CD:637908|(248)489-6000^CD:170||CD:151|M|CD:3391461|606831661088^^^DONOTSEND^FIN
NBR^CD:237968946||||CD:654655774|||0|||CD:654897458\r"
+
"PV1|1|Inpatient|MS^0414^1^CL^^^MMCCN|3|||5332^Rahiman^Abdul|||MED|MS|||1|||5332^Rahiman^Doctor|A||60|||||||||||||||||||CL||Active|||20110329113000\r"
+
"ORC|NW|3415770735^HNAM_ORDERID|||RL||||20110628095142|71573^Doctor^Janet^D^^^^^DONOTSEND^^^^COMMUNITY
DR NBR~70988^Doctor^Janet^D^^^^^DONOTSEND^^^^Personnel Primary
Identifier~FHJDB2293^Doctor^Janet^D^^^^^DONOTSEND^^^^External
Identifier~T^Doctor^Janet^D^^^^^DONOTSEND^^^^CD:296695676|||||20110628095231|||CD:2562^Written|71573^Doctor^Janet^D^^^^^DONOTSEND^^^^COMMUNITY
DR NBR~70988^Doctor^Janet^D^^^^^DONOTSEND^^^^Personnel Primary
Identifier~FHJDB2293^Doctor^Janet^D^^^^^DONOTSEND^^^^External
Identifier~T^Doctor^Janet^D^^^^^DONOTSEND^^^^CD:296695676\r"
+ "OBR|1|3415770735^HNAM_ORDERID||CL987^MRA Head w and w/o
Contrast|||||||||||Rad Type&Rad
Type|||||00000MR20110001703^HNA_ACCN~8546871^HNA_ACCNID~7515376^HNA_PACSID|CD:232990825|20110628095231||Magnetic
Resonance Imaging|||1^^0^20110628095100^^RT||||^Dizziness\r"
+ "OBX|1|TX|20725^ROUTINE
HEMATOLOGY|H7800-4|This~Is~A~Report~~~~~||||||I|||200704021122\r"
+ "NTE|1|P|Special Instructions-\r";
Parser p = new GenericParser();
Message hapiMsg;
// The parse method performs the actual parsing
hapiMsg = p.parse(msg);
ORU_R01_OBSERVATION obx = ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0);
assertEquals("This",
obx.getOBX().getObx5_ObservationValue()[0].encode());
assertEquals("Is", obx.getOBX().getObx5_ObservationValue()[1].encode());
assertEquals("A", obx.getOBX().getObx5_ObservationValue()[2].encode());
assertEquals("Report",
obx.getOBX().getObx5_ObservationValue()[3].encode());
assertEquals("", obx.getOBX().getObx5_ObservationValue()[4].encode());
assertEquals("", obx.getOBX().getObx5_ObservationValue()[5].encode());
assertEquals("", obx.getOBX().getObx5_ObservationValue()[6].encode());
assertEquals("", obx.getOBX().getObx5_ObservationValue()[7].encode());
Cheers,
James
On Mon, Nov 30, 2015 at 10:59 PM, Ian Vowles
<ian.vow...@health.qld.gov.au<mailto:ian.vow...@health.qld.gov.au>> wrote:
We have been having some trouble with textual OBX-5’s which have repeats used
to indicate each line of a report when some empty repeats exist to denote empty
lines for formatting.
Is there a way to overcome this?
The following example demonstrates the problem
Thanks
Ian
package hapiexamples;
import ca.uhn.hl7v2.HL7Exception;
import ca.uhn.hl7v2.app.ApplicationException;
import ca.uhn.hl7v2.model.Message;
import ca.uhn.hl7v2.model.v24.message.ORU_R01;
import ca.uhn.hl7v2.parser.GenericParser;
import ca.uhn.hl7v2.parser.Parser;
import java.io.IOException;
/**
*
* @author VowlesI
*/
public class OruR01RepeatsInObx5 {
public static void main(String[] args) throws HL7Exception,
ApplicationException, IOException {
String msg =
"MSH|^~\\&|HNAM|CL|CL_RADNET|CL|20110628095233||ORU^R01|Q2301030099T1904270849|P|2.4\r"
+ "PID|1||10011682^^^CL_MRN
Pool^^CD:237968946|60683166^^^DONOTSEND^^CD:237968946|CLABTEST^ONE||19500101120000|F||C|34605
W 12 MILE RD^^FARM
MILLS^MN^48331-3263^CD:309221^CD:756^^CD:637908|CD:637908|(248)489-6000^CD:170||CD:151|M|CD:3391461|606831661088^^^DONOTSEND^FIN
NBR^CD:237968946||||CD:654655774|||0|||CD:654897458\r"
+
"PV1|1|Inpatient|MS^0414^1^CL^^^MMCCN|3|||5332^Rahiman^Abdul|||MED|MS|||1|||5332^Rahiman^Doctor|A||60|||||||||||||||||||CL||Active|||20110329113000\r"
+
"ORC|NW|3415770735^HNAM_ORDERID|||RL||||20110628095142|71573^Doctor^Janet^D^^^^^DONOTSEND^^^^COMMUNITY
DR NBR~70988^Doctor^Janet^D^^^^^DONOTSEND^^^^Personnel Primary
Identifier~FHJDB2293^Doctor^Janet^D^^^^^DONOTSEND^^^^External
Identifier~T^Doctor^Janet^D^^^^^DONOTSEND^^^^CD:296695676|||||20110628095231|||CD:2562^Written|71573^Doctor^Janet^D^^^^^DONOTSEND^^^^COMMUNITY
DR NBR~70988^Doctor^Janet^D^^^^^DONOTSEND^^^^Personnel Primary
Identifier~FHJDB2293^Doctor^Janet^D^^^^^DONOTSEND^^^^External
Identifier~T^Doctor^Janet^D^^^^^DONOTSEND^^^^CD:296695676\r"
+ "OBR|1|3415770735^HNAM_ORDERID||CL987^MRA Head w and w/o
Contrast|||||||||||Rad Type&Rad
Type|||||00000MR20110001703^HNA_ACCN~8546871^HNA_ACCNID~7515376^HNA_PACSID|CD:232990825|20110628095231||Magnetic
Resonance Imaging|||1^^0^20110628095100^^RT||||^Dizziness\r"
+ "OBX|1|TX|20725^ROUTINE
HEMATOLOGY|H7800-4|This~Is~A~Report~~~~~||||||I|||200704021122\r"
+ "NTE|1|P|Special Instructions-\r";
Parser p = new GenericParser();
Message hapiMsg;
// The parse method performs the actual parsing
hapiMsg = p.parse(msg);
System.out.println("OBX-5 has " + ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0).getOBX().getObx5_ObservationValueReps());
hapiMsg.parse(hapiMsg.encode());
System.out.println("OBX-5 has " + ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0).getOBX().getObx5_ObservationValueReps());
hapiMsg.parse(hapiMsg.encode());
System.out.println("OBX-5 has " + ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0).getOBX().getObx5_ObservationValueReps());
hapiMsg.parse(hapiMsg.encode());
System.out.println("OBX-5 has " + ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0).getOBX().getObx5_ObservationValueReps());
hapiMsg.parse(hapiMsg.encode());
System.out.println("OBX-5 has " + ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0).getOBX().getObx5_ObservationValueReps());
hapiMsg.parse(hapiMsg.encode());
System.out.println("OBX-5 has " + ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0).getOBX().getObx5_ObservationValueReps());
hapiMsg.parse(hapiMsg.encode());
System.out.println("OBX-5 has " + ((ORU_R01)
hapiMsg).getPATIENT_RESULT(0).getORDER_OBSERVATION(0).getOBSERVATION(0).getOBX().getObx5_ObservationValueReps());
}
}
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