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NIFI-12520: ExtractHL7Attributes processor ignores repeatable field values

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This closes #8167.

Signed-off-by: Peter Turcsanyi <turcsanyi@apache.org>

(cherry picked from commit 16d170fdfdbc12723746ae1f7ae8568246227ab2)
This commit is contained in:
Mark Bathori 2023-12-15 22:41:17 +01:00 committed by Peter Turcsanyi
parent 98b0ceffd8
commit 6a3301dfbf
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GPG Key ID: 55A813F1C3E553DC
2 changed files with 100 additions and 47 deletions
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20
nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/main/java/org/apache/nifi/processors/hl7/ExtractHL7Attributes.java
View File

@ -281,8 +281,8 @@ public class ExtractHL7Attributes extends AbstractProcessor {
final Map<String, Type> fields = new TreeMap<>();
final String[] segmentNames = segment.getNames();
for (int i = 1; i <= segment.numFields(); i++) {
final Type field = segment.getField(i, 0);
if (!isEmpty(field)) {
final Type[] fieldValues = segment.getField(i);
if (fieldValues != null && fieldValues.length != 0) {
final String fieldName;
//Some user defined segments (e.g. Z segments) will not have corresponding names returned
//from segment.getNames() above. If we encounter one of these, do the next best thing
@ -294,13 +294,17 @@ public class ExtractHL7Attributes extends AbstractProcessor {
fieldName = String.valueOf(i);
}
final String fieldKey = new StringBuilder()
.append(segmentKey)
.append(".")
.append(fieldName)
.toString();
final String fieldKey = String.format("%s.%s", segmentKey, fieldName);
fields.put(fieldKey, field);
//Checks if the field is repeatable, if the max cardinality value is 0 or more than 1 then the field is repeatable
if (segment.getMaxCardinality(i) == 1) {
fields.put(fieldKey, fieldValues[0]);
} else {
for (int j = 0; j < fieldValues.length; j++) {
final String repeatableFieldKey = String.format("%s_%s", fieldKey, j + 1);
fields.put(repeatableFieldKey, fieldValues[j]);
}
}
}
}
return fields;

127
nifi-nar-bundles/nifi-hl7-bundle/nifi-hl7-processors/src/test/java/org/apache/nifi/processors/hl7/TestExtractHL7Attributes.java
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@ -22,7 +22,6 @@ import org.apache.nifi.util.TestRunners;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.Map;
import java.util.SortedMap;
@ -105,17 +104,17 @@ public class TestExtractHL7Attributes {
expectedAttributes.put("MSH.12", "2.3");
expectedAttributes.put("ORC_1.1", "NW");
expectedAttributes.put("ORC_1.2", "987654321^EPC");
expectedAttributes.put("ORC_1.2_1", "987654321^EPC");
expectedAttributes.put("ORC_1.3", "123456789^EPC");
expectedAttributes.put("ORC_1.9", "20161003000000");
expectedAttributes.put("ORC_1.12", "SMITH");
expectedAttributes.put("ORC_1.12_1", "SMITH");
expectedAttributes.put("OBR_1.1", "1");
expectedAttributes.put("OBR_1.2", "341856649^HNAM_ORDERID");
expectedAttributes.put("OBR_1.2_1", "341856649^HNAM_ORDERID");
expectedAttributes.put("OBR_1.3", "000000000000000000");
expectedAttributes.put("OBR_1.4", "648088^Basic Metabolic Panel");
expectedAttributes.put("OBR_1.7", "20150101000000");
expectedAttributes.put("OBR_1.16", "1620^Johnson^Corey^A");
expectedAttributes.put("OBR_1.16_1", "1620^Johnson^Corey^A");
expectedAttributes.put("OBR_1.22", "20150101000000");
expectedAttributes.put("OBR_1.25", "F");
expectedAttributes.put("OBR_1.36", "20150101000000");
@ -124,16 +123,16 @@ public class TestExtractHL7Attributes {
expectedAttributes.put("OBX_1.2", "NM");
expectedAttributes.put("OBX_1.3", "GLU^Glucose Lvl");
expectedAttributes.put("OBX_1.4", "59");
expectedAttributes.put("OBX_1.5", "mg/dL");
expectedAttributes.put("OBX_1.5_1", "mg/dL");
expectedAttributes.put("OBX_1.6", "65-99^65^99");
expectedAttributes.put("OBX_1.7", "L");
expectedAttributes.put("OBX_1.10", "F");
expectedAttributes.put("OBX_1.13", "20150102000000");
expectedAttributes.put("PD1.4", "1234567890^LAST^FIRST^M^^^^^NPI");
expectedAttributes.put("PD1.4_1", "1234567890^LAST^FIRST^M^^^^^NPI");
expectedAttributes.put("PID.3", "12345^^^XYZ^MR");
expectedAttributes.put("PID.5", "SMITH^JOHN");
expectedAttributes.put("PID.3_1", "12345^^^XYZ^MR");
expectedAttributes.put("PID.5_1", "SMITH^JOHN");
expectedAttributes.put("PID.7", "19700100");
expectedAttributes.put("PID.8", "M");
expectedAttributes.put("PID.18", "111111111111");
@ -143,7 +142,7 @@ public class TestExtractHL7Attributes {
}
@Test
public void testExtractWithSegmentNames() throws IOException {
public void testExtractWithSegmentNames() {
final String message = "MSH|^~\\&|XXXXXXXX||HealthProvider||||ORU^R01|Q1111111111111111111|P|2.3|\r\n" +
"PID|||12345^^^XYZ^MR||SMITH^JOHN||19700100|M||||||||||111111111111|123456789|\r\n" +
"PD1||||1234567890^LAST^FIRST^M^^^^^NPI|\r\n" +
@ -163,17 +162,17 @@ public class TestExtractHL7Attributes {
expectedAttributes.put("MSH.VersionID", "2.3");
expectedAttributes.put("ORC_1.OrderControl", "NW");
expectedAttributes.put("ORC_1.PlacerOrderNumber", "987654321^EPC");
expectedAttributes.put("ORC_1.PlacerOrderNumber_1", "987654321^EPC");
expectedAttributes.put("ORC_1.FillerOrderNumber", "123456789^EPC");
expectedAttributes.put("ORC_1.DateTimeOfTransaction", "20161003000000");
expectedAttributes.put("ORC_1.OrderingProvider", "SMITH");
expectedAttributes.put("ORC_1.OrderingProvider_1", "SMITH");
expectedAttributes.put("OBR_1.SetIDObservationRequest", "1");
expectedAttributes.put("OBR_1.PlacerOrderNumber", "341856649^HNAM_ORDERID");
expectedAttributes.put("OBR_1.PlacerOrderNumber_1", "341856649^HNAM_ORDERID");
expectedAttributes.put("OBR_1.FillerOrderNumber", "000000000000000000");
expectedAttributes.put("OBR_1.UniversalServiceIdentifier", "648088^Basic Metabolic Panel");
expectedAttributes.put("OBR_1.ObservationDateTime", "20150101000000");
expectedAttributes.put("OBR_1.OrderingProvider", "1620^Johnson^Corey^A");
expectedAttributes.put("OBR_1.OrderingProvider_1", "1620^Johnson^Corey^A");
expectedAttributes.put("OBR_1.ResultsRptStatusChngDateTime", "20150101000000");
expectedAttributes.put("OBR_1.ResultStatus", "F");
expectedAttributes.put("OBR_1.ScheduledDateTime", "20150101000000");
@ -182,16 +181,16 @@ public class TestExtractHL7Attributes {
expectedAttributes.put("OBX_1.ValueType", "NM");
expectedAttributes.put("OBX_1.ObservationIdentifier", "GLU^Glucose Lvl");
expectedAttributes.put("OBX_1.ObservationSubID", "59");
expectedAttributes.put("OBX_1.ObservationValue", "mg/dL");
expectedAttributes.put("OBX_1.ObservationValue_1", "mg/dL");
expectedAttributes.put("OBX_1.Units", "65-99^65^99");
expectedAttributes.put("OBX_1.ReferencesRange", "L");
expectedAttributes.put("OBX_1.NatureOfAbnormalTest", "F");
expectedAttributes.put("OBX_1.UserDefinedAccessChecks", "20150102000000");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo", "1234567890^LAST^FIRST^M^^^^^NPI");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo_1", "1234567890^LAST^FIRST^M^^^^^NPI");
expectedAttributes.put("PID.PatientIDInternalID", "12345^^^XYZ^MR");
expectedAttributes.put("PID.PatientName", "SMITH^JOHN");
expectedAttributes.put("PID.PatientIDInternalID_1", "12345^^^XYZ^MR");
expectedAttributes.put("PID.PatientName_1", "SMITH^JOHN");
expectedAttributes.put("PID.DateOfBirth", "19700100");
expectedAttributes.put("PID.Sex", "M");
expectedAttributes.put("PID.PatientAccountNumber", "111111111111");
@ -201,7 +200,7 @@ public class TestExtractHL7Attributes {
}
@Test
public void testExtractWithSegmentNamesAndFields() throws IOException {
public void testExtractWithSegmentNamesAndFields() {
final String message = "MSH|^~\\&|XXXXXXXX||HealthProvider||||ORU^R01|Q1111111111111111111|P|2.3|\r\n" +
"PID|||12345^^^XYZ^MR||SMITH^JOHN||19700100|M||||||||||111111111111|123456789|\r\n" +
"PD1||||1234567890^LAST^FIRST^M^^^^^NPI|\r\n" +
@ -222,24 +221,24 @@ public class TestExtractHL7Attributes {
expectedAttributes.put("MSH.VersionID", "2.3");
expectedAttributes.put("ORC_1.OrderControl", "NW");
expectedAttributes.put("ORC_1.PlacerOrderNumber.EntityIdentifier", "987654321");
expectedAttributes.put("ORC_1.PlacerOrderNumber.NamespaceID", "EPC");
expectedAttributes.put("ORC_1.PlacerOrderNumber_1.EntityIdentifier", "987654321");
expectedAttributes.put("ORC_1.PlacerOrderNumber_1.NamespaceID", "EPC");
expectedAttributes.put("ORC_1.FillerOrderNumber.EntityIdentifier", "123456789");
expectedAttributes.put("ORC_1.FillerOrderNumber.NamespaceID", "EPC");
expectedAttributes.put("ORC_1.DateTimeOfTransaction", "20161003000000");
expectedAttributes.put("ORC_1.OrderingProvider.IDNumber", "SMITH");
expectedAttributes.put("ORC_1.OrderingProvider_1.IDNumber", "SMITH");
expectedAttributes.put("OBR_1.SetIDObservationRequest", "1");
expectedAttributes.put("OBR_1.PlacerOrderNumber.EntityIdentifier", "341856649");
expectedAttributes.put("OBR_1.PlacerOrderNumber.NamespaceID", "HNAM_ORDERID");
expectedAttributes.put("OBR_1.PlacerOrderNumber_1.EntityIdentifier", "341856649");
expectedAttributes.put("OBR_1.PlacerOrderNumber_1.NamespaceID", "HNAM_ORDERID");
expectedAttributes.put("OBR_1.FillerOrderNumber.EntityIdentifier", "000000000000000000");
expectedAttributes.put("OBR_1.UniversalServiceIdentifier.Identifier", "648088");
expectedAttributes.put("OBR_1.UniversalServiceIdentifier.Text", "Basic Metabolic Panel");
expectedAttributes.put("OBR_1.ObservationDateTime", "20150101000000");
expectedAttributes.put("OBR_1.OrderingProvider.IDNumber", "1620");
expectedAttributes.put("OBR_1.OrderingProvider.FamilyName", "Johnson");
expectedAttributes.put("OBR_1.OrderingProvider.GivenName", "Corey");
expectedAttributes.put("OBR_1.OrderingProvider.MiddleInitialOrName", "A");
expectedAttributes.put("OBR_1.OrderingProvider_1.IDNumber", "1620");
expectedAttributes.put("OBR_1.OrderingProvider_1.FamilyName", "Johnson");
expectedAttributes.put("OBR_1.OrderingProvider_1.GivenName", "Corey");
expectedAttributes.put("OBR_1.OrderingProvider_1.MiddleInitialOrName", "A");
expectedAttributes.put("OBR_1.ResultsRptStatusChngDateTime", "20150101000000");
expectedAttributes.put("OBR_1.ResultStatus", "F");
expectedAttributes.put("OBR_1.ScheduledDateTime", "20150101000000");
@ -249,7 +248,7 @@ public class TestExtractHL7Attributes {
expectedAttributes.put("OBX_1.ObservationIdentifier.Identifier", "GLU");
expectedAttributes.put("OBX_1.ObservationIdentifier.Text", "Glucose Lvl");
expectedAttributes.put("OBX_1.ObservationSubID", "59");
expectedAttributes.put("OBX_1.ObservationValue", "mg/dL");
expectedAttributes.put("OBX_1.ObservationValue_1", "mg/dL");
expectedAttributes.put("OBX_1.Units.Identifier", "65-99");
expectedAttributes.put("OBX_1.Units.Text", "65");
expectedAttributes.put("OBX_1.Units.NameOfCodingSystem", "99");
@ -257,17 +256,17 @@ public class TestExtractHL7Attributes {
expectedAttributes.put("OBX_1.NatureOfAbnormalTest", "F");
expectedAttributes.put("OBX_1.UserDefinedAccessChecks", "20150102000000");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.IDNumber", "1234567890");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.FamilyName", "LAST");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.GivenName", "FIRST");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.MiddleInitialOrName", "M");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo.AssigningAuthority", "NPI");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo_1.IDNumber", "1234567890");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo_1.FamilyName", "LAST");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo_1.GivenName", "FIRST");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo_1.MiddleInitialOrName", "M");
expectedAttributes.put("PD1.PatientPrimaryCareProviderNameIDNo_1.AssigningAuthority", "NPI");
expectedAttributes.put("PID.PatientIDInternalID.ID", "12345");
expectedAttributes.put("PID.PatientIDInternalID.AssigningAuthority", "XYZ");
expectedAttributes.put("PID.PatientIDInternalID.IdentifierTypeCode", "MR");
expectedAttributes.put("PID.PatientName.FamilyName", "SMITH");
expectedAttributes.put("PID.PatientName.GivenName", "JOHN");
expectedAttributes.put("PID.PatientIDInternalID_1.ID", "12345");
expectedAttributes.put("PID.PatientIDInternalID_1.AssigningAuthority", "XYZ");
expectedAttributes.put("PID.PatientIDInternalID_1.IdentifierTypeCode", "MR");
expectedAttributes.put("PID.PatientName_1.FamilyName", "SMITH");
expectedAttributes.put("PID.PatientName_1.GivenName", "JOHN");
expectedAttributes.put("PID.DateOfBirth", "19700100");
expectedAttributes.put("PID.Sex", "M");
expectedAttributes.put("PID.PatientAccountNumber.ID", "111111111111");
@ -276,4 +275,54 @@ public class TestExtractHL7Attributes {
runTests(message, expectedAttributes, true, true);
}
@Test
public void testExtractWithRepeatableField() {
final String message = "MSH|^~\\&|XXXXXXXX||HealthProvider||||SIU^S12|Q1111111111111111111|P|2.5.1|\r\n" +
"AIP|1||123456^SMITH^JOHN^A^^^^^NPI^^^^NPI~123457^SMITH^JOHN^A^^^^^OD^^^^OD~123458^SMITH^JOHN^A^^^^^MD^^^^MD|100^M.D.||20231010133000|0|MIN|45|MIN\r\n";
final SortedMap<String, String> expectedAttributes = new TreeMap<>();
expectedAttributes.put("MSH.FieldSeparator", "|");
expectedAttributes.put("MSH.EncodingCharacters", "^~\\&");
expectedAttributes.put("MSH.SendingApplication.NamespaceID", "XXXXXXXX");
expectedAttributes.put("MSH.ReceivingApplication.NamespaceID", "HealthProvider");
expectedAttributes.put("MSH.MessageType.MessageCode", "SIU");
expectedAttributes.put("MSH.MessageType.TriggerEvent", "S12");
expectedAttributes.put("MSH.MessageControlID", "Q1111111111111111111");
expectedAttributes.put("MSH.ProcessingID.ProcessingID", "P");
expectedAttributes.put("MSH.VersionID.VersionID", "2.5.1");
expectedAttributes.put("AIP.Duration", "45");
expectedAttributes.put("AIP.DurationUnits.Identifier", "MIN");
expectedAttributes.put("AIP.ResourceType.Identifier", "100");
expectedAttributes.put("AIP.ResourceType.Text", "M.D.");
expectedAttributes.put("AIP.SetIDAIP", "1");
expectedAttributes.put("AIP.StartDateTime", "20231010133000");
expectedAttributes.put("AIP.StartDateTimeOffset", "0");
expectedAttributes.put("AIP.StartDateTimeOffsetUnits.Identifier", "MIN");
expectedAttributes.put("AIP.PersonnelResourceID_1.AssigningAuthority", "NPI");
expectedAttributes.put("AIP.PersonnelResourceID_1.FamilyName", "SMITH");
expectedAttributes.put("AIP.PersonnelResourceID_1.GivenName", "JOHN");
expectedAttributes.put("AIP.PersonnelResourceID_1.IDNumber", "123456");
expectedAttributes.put("AIP.PersonnelResourceID_1.IdentifierTypeCode", "NPI");
expectedAttributes.put("AIP.PersonnelResourceID_1.SecondAndFurtherGivenNamesOrInitialsThereof", "A");
expectedAttributes.put("AIP.PersonnelResourceID_2.AssigningAuthority", "OD");
expectedAttributes.put("AIP.PersonnelResourceID_2.FamilyName", "SMITH");
expectedAttributes.put("AIP.PersonnelResourceID_2.GivenName", "JOHN");
expectedAttributes.put("AIP.PersonnelResourceID_2.IDNumber", "123457");
expectedAttributes.put("AIP.PersonnelResourceID_2.IdentifierTypeCode", "OD");
expectedAttributes.put("AIP.PersonnelResourceID_2.SecondAndFurtherGivenNamesOrInitialsThereof", "A");
expectedAttributes.put("AIP.PersonnelResourceID_3.AssigningAuthority", "MD");
expectedAttributes.put("AIP.PersonnelResourceID_3.FamilyName", "SMITH");
expectedAttributes.put("AIP.PersonnelResourceID_3.GivenName", "JOHN");
expectedAttributes.put("AIP.PersonnelResourceID_3.IDNumber", "123458");
expectedAttributes.put("AIP.PersonnelResourceID_3.IdentifierTypeCode", "MD");
expectedAttributes.put("AIP.PersonnelResourceID_3.SecondAndFurtherGivenNamesOrInitialsThereof", "A");
runTests(message, expectedAttributes, true, true);
}
}