GilmoreA6
commented
1 month ago After further research, RS does not use the LINUX4HEALTH HL7->FHIR mappings (https://github.com/LinuxForHealth/hl7v2-fhir-converter/tree/master/src/main/java/io/github/linuxforhealth/hl7) unless the message type is not mapped in RS (i.e. ADT-A04 would use the LINX4HEALTH library but ORU_RO1 would not). For the NM data type for OBX.5 RS is simply taking the string value of the inbound OBX.5 and placing it into the valueQuantity.value fhir element.
This limits our potential options to solve the leading zero issue to the following:
1.) Ask RS to change how it is converting the OBX.5 value for the NM data type to a valueString FHIR element in a new custom extension.
Pros:
- retains original value that was sent in OBX-5
- applies to all senders uniformly without further configuration needed
Cons:
- does not follow official hl7 V2 -> fhir mappings
- timeline for implementation unclear as it requires RS agreement
2.) Create sender transform that moves value in valueQuantity,value to valueString element on same observation resource
Pros:
- retains original value that was sent in OBX-5
Cons:
- does not follow official hl7 V2 -> fhir mappings
- requires both a sender and a receiver transform
- Create a sender transform that removes leading zeroes in valueQuantity.value
Pros:
- Easy to implement and change
- requires only a sender transform
- makes value conform to FHIR R4 standard
Cons:
- does not maintain original value sent by sender
- transform needs to be applied to each sender in sender settings individually
basiliskus
Bug
Describe the Bug
When an OBX segment has a data type of "NM" in OBX-2 and the result value in OBX-5 contains leading zeros, the resulting fhir bundle contains an invalid value for "Bundle.entry.resource.ofType(Observation).valueQuantity.value".
example HL7 segment:
OBX|1|NM|38473-5^17-Hydroxyprogesterone^LN|1|065.88|nmol/L|<85|N|||F|||20241015055726
example converted FHIR Resource:
{ "fullUrl": "Observation/1729104155244834642.39eac40b-c44b-4d07-b4bb-8b96ade62411", "resource": { "resourceType": "Observation", "id": "1729104155244834642.39eac40b-c44b-4d07-b4bb-8b96ade62411", "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/sub-id", "valueString": "1" }, { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/obx-observation", "extension": [ { "url": "OBX.2", "valueId": "NM" }, { "url": "OBX.6", "valueCodeableConcept": { "coding": [ { "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", "valueString": "coding" } ], "code": "nmol/L" } ] } }, { "url": "OBX.11", "valueString": "F" } ] } ], "status": "final", "code": { "coding": [ { "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", "valueString": "coding" }, { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding-system", "valueString": "LN" } ], "system": "http://loinc.org", "code": "38473-5", "display": "17-Hydroxyprogesterone" } ] }, "subject": { "reference": "Patient/1729104154973770467.0f02574a-aaca-4e07-9989-d810f3a7d499" }, "effectiveDateTime": "2024-10-15T05:57:26Z", "_effectiveDateTime": { "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/hl7v2-date-time", "valueString": "20241015055726" } ] }, "valueQuantity": { "value": 065.88, "unit": "nmol/L" }, "interpretation": [ { "coding": [ { "extension": [ { "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/cwe-coding", "valueString": "coding" } ], "code": "N" } ] } ], "referenceRange": [ { "text": "<85" } ] } }This occurs because leading zeros are not explicitly invalid in HL7 V2 NM data type (https://hl7-definition.caristix.com/v2/HL7v2.7/DataTypes/NM)
, however when this is converted to FHIR per the hl7V2 -> FHIR documentation (https://build.fhir.org/ig/HL7/v2-to-fhir/ConceptMap-segment-obx-to-observation.html) this becomes a ValueQuantity.value element (https://hl7.org/fhir/R4/datatypes.html#Quantity) with a primitive type of decimal,
which does not allow leading zeros (https://www.w3.org/TR/xmlschema-2/)
Impact
When an HL7 V2 message is sent into ReportStream and converted to FHIR exception "ca.uhn.fhir.parser.DataFormatException: HAPI-1861: Failed to parse JSON encoded FHIR content: Invalid numeric value: Leading zeroes not allowed at [line: 1, column: 137695]" is thrown when attempting to parse the FHIR bundle to apply the jurisdictional filters.
To Reproduce
Expected Behavior
The resulting FHIR resource from a converted HL7 v2 message should not contain invalid values and should not throw an error when reaching the destination-filter step
Acceptance Criteria
Tasks
Engineering