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feat: add message line numbers to v2 json
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@mechanik-daniel
mechanik-daniel committed Aug 22, 2024
1 parent d54a4c1 commit 5c8045b
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Showing 3 changed files with 209 additions and 3 deletions.
10 changes: 7 additions & 3 deletions src/helpers/jsonataExpression.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -186,17 +186,21 @@ const expressions: InternalJsonataExpression = {
)};
$translateSegment := function($segment){(
$line := $segment.MessageLine;
$segId := $segment.\`0\`;
$segDef := $getSegmentDef($segId, $v2version);
$segment.fields#$i[$i>0].$translateField($, $segDef, $i-1){
'SegmentDescription': $segDef.desc,
'MessageLine': $line,
$normalizeKey(name): value
}
)};
$rawJson.segments@$s.$translateSegment($s){
$segmentsWithLines := $rawJson.segments#$line.($merge([$, {'MessageLine': $line+1}]));
$segmentsWithLines@$s.$translateSegment($s){
$s.\`0\`: $
};
};
)`),
parseFumeExpression: jsonata(`
(
Expand Down
7 changes: 7 additions & 0 deletions tests/fhir/inputs/HL7-v2-LineNumbering.txt
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Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
MSH|^~\&|1^Autolab^3.02|110^some_place|34^HL7_PDF|2400^HL7_PDF|20240726083203||ORU^R01|12345678|P|2.3||0^^||||||5||
ORC||2222222222^^^^^^^|||CM||||20240725154900|207^first^last^^^^||1234567^first^last|||||general^^^^||^|N|N|555555555|N^Y||403aa3gec5fb33efd666666cd45b1e5a|
NTE||O| Clinical_diagnosis:MDS|0|
OBR|1||830814256^^^^^^^||||20240718195000||0^|^^auto^^^^||||20240718210300|0^^^^^^^||||||||||||^^0^^^^^^|||||||||||||||||0|4^green^^^^|1^Blood^^^^|
NTE|15151515|O|new_sample|1|
OBX|10|TX|0813321000^esccol^^^Escherichia coli^||.|0^""^^^^|^|N|||F|M|104^714^ Micro_lab|20240725154900|9999^Micro|1234567-8^First^last^^^^^||0|0^^^^^|^AutoComm^16^^^^^|9999^Micro^^^^|207^general^^^^||0810109809^genct^^^^||1|^system^routing^^^^^|20240725150000|^^|N|1111111111|2222222222|33333333333|
NTE|15471137|O|updated_result|1|
195 changes: 195 additions & 0 deletions tests/root/hl7.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -329,6 +329,7 @@ describe('HL7 v2 tests', () => {
expect(res.body).toStrictEqual({
MSH: {
SegmentDescription: 'Message Header',
MessageLine: 1,
FieldSeparator: '|',
EncodingCharacters: '^~\\&',
SendingApplication: {
Expand Down Expand Up @@ -357,6 +358,7 @@ describe('HL7 v2 tests', () => {
},
PID: {
SegmentDescription: 'Patient Identification',
MessageLine: 2,
SetID: '58705',
PatientID: {
IDNumber: '58705'
Expand Down Expand Up @@ -394,6 +396,7 @@ describe('HL7 v2 tests', () => {
},
PV1: {
SegmentDescription: 'Patient Visit',
MessageLine: 3,
PatientClass: '1',
AssignedPatientLocation: {
PointOfCare: 'CE'
Expand All @@ -415,6 +418,7 @@ describe('HL7 v2 tests', () => {
OBX: [
{
SegmentDescription: 'Observation/Result',
MessageLine: 4,
SetID: '1',
ValueType: 'NM',
ObservationIdentifier: {
Expand All @@ -435,6 +439,7 @@ describe('HL7 v2 tests', () => {
},
{
SegmentDescription: 'Observation/Result',
MessageLine: 5,
SetID: '2',
ValueType: 'NM',
ObservationIdentifier: {
Expand Down Expand Up @@ -548,6 +553,7 @@ describe('HL7 v2 tests', () => {
expect(res.body).toStrictEqual({
MSH: {
SegmentDescription: 'Message header segment',
MessageLine: 1,
FieldSeparator: '|',
EncodingCharacters: '^~\\&',
SendingApplication: {
Expand Down Expand Up @@ -584,6 +590,7 @@ describe('HL7 v2 tests', () => {
},
OBX: {
SegmentDescription: 'Observation segment',
MessageLine: 2,
SetID: '10',
ValueType: 'TX',
ObservationIdentifier: {
Expand Down Expand Up @@ -632,4 +639,192 @@ describe('HL7 v2 tests', () => {
}
});
});

test('HL7 v2 line numbering', async () => {
const input = getResourceFileContents('inputs', 'HL7-v2-LineNumbering.txt');
const requestBody = {
input,
contentType: 'x-application/hl7-v2+er7',
fume: '$'
};

const res = await request(globalThis.app).post('/').send(requestBody);

expect(res.body).toStrictEqual(
{
MSH: {
SegmentDescription: 'Message header segment',
MessageLine: 1,
FieldSeparator: '|',
EncodingCharacters: '^~\\&',
SendingApplication: {
NamespaceID: '1',
UniversalID: 'Autolab',
UniversalIDType: '3.02'
},
SendingFacility: {
NamespaceID: '110',
UniversalID: 'some_place'
},
ReceivingApplication: {
NamespaceID: '34',
UniversalID: 'HL7_PDF'
},
ReceivingFacility: {
NamespaceID: '2400',
UniversalID: 'HL7_PDF'
},
DateTimeOfMessage: {
TimeOfAnEvent: '20240726083203'
},
MessageType: {
MessageType: 'ORU',
TriggerEvent: 'R01'
},
MessageControlID: '12345678',
ProcessingID: {
ProcessingID: 'P'
},
VersionID: '2.3',
ContinuationPointer: '0^^',
MSH20: '5'
},
ORC: {
SegmentDescription: 'Common order segment',
MessageLine: 2,
PlacerOrderNumber: {
EntityIdentifier: '2222222222'
},
OrderStatus: 'CM',
DateTimeOfTransaction: {
TimeOfAnEvent: '20240725154900'
},
EnteredBy: {
IDNumber: '207',
FamilyName: 'first',
GivenName: 'last'
},
OrderingProvider: {
IDNumber: '1234567',
FamilyName: 'first',
GivenName: 'last'
},
EnteringOrganization: {
Identifier: 'general'
},
ORC20: 'N',
ORC21: 'N',
ORC22: '555555555',
ORC23: 'N^Y',
ORC25: '403aa3gec5fb33efd666666cd45b1e5a'
},
NTE: [
{
SegmentDescription: 'Notes and comments segment',
MessageLine: 3,
SourceOfComment: 'O',
Comment: ' Clinical_diagnosis:MDS',
NTE4: '0'
},
{
SegmentDescription: 'Notes and comments segment',
MessageLine: 5,
SetID: '15151515',
SourceOfComment: 'O',
Comment: 'new_sample',
NTE4: '1'
},
{
SegmentDescription: 'Notes and comments segment',
MessageLine: 7,
SetID: '15471137',
SourceOfComment: 'O',
Comment: 'updated_result',
NTE4: '1'
}
],
OBR: {
SegmentDescription: 'Observation request segment',
MessageLine: 4,
SetID: '1',
FillerOrderNumber: {
EntityIdentifier: '830814256'
},
ObservationDateTime: {
TimeOfAnEvent: '20240718195000'
},
CollectionVolume: {
Quantity: '0'
},
CollectorIdentifier: {
GivenName: 'auto'
},
SpecimenReceivedDateTime: {
TimeOfAnEvent: '20240718210300'
},
SpecimenSource: {
SpecimenSourceNameOrCode: {
Identifier: '0'
}
},
Quantity_Timing: {
Duration: '0'
},
OBR44: '0',
OBR45: '4^green^^^^',
OBR46: '1^Blood^^^^'
},
OBX: {
SegmentDescription: 'Observation segment',
MessageLine: 6,
SetID: '10',
ValueType: 'TX',
ObservationIdentifier: {
Identifier: '0813321000',
Text: 'esccol',
AlternateText: 'Escherichia coli'
},
ObservationValue: '.',
Units: {
Identifier: '0',
Text: '""'
},
ReferencesRange: '^',
AbnormalFlags: 'N',
ObservResultStatus: 'F',
DateLastObsNormalValues: {
TimeOfAnEvent: 'M'
},
UserDefinedAccessChecks: '104^714^ Micro_lab',
DateTimeOfTheObservation: {
TimeOfAnEvent: '20240725154900'
},
ProducersID: {
Identifier: '9999',
Text: 'Micro'
},
ResponsibleObserver: {
IDNumber: '1234567-8',
FamilyName: 'First',
GivenName: 'last'
},
OBX18: '0',
OBX19: '0^^^^^',
OBX20: '^AutoComm^16^^^^^',
OBX21: '9999^Micro^^^^',
OBX22: '207^general^^^^',
OBX24: '0810109809^genct^^^^',
OBX26: '1',
OBX27: '^system^routing^^^^^',
OBX28: '20240725150000',
OBX29: '^^',
OBX30: 'N',
OBX31: '1111111111',
OBX32: '2222222222',
OBX33: '33333333333'
}
});
}

);
});

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