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fix: Update message parser fields pt.2 #1500

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fix: Update message parser fields pt.2 #1500

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db2d23e
fix reason for visit
angelathe Jun 3, 2026
64b32b1
fix specimen type and specimen collection date
angelathe Jun 4, 2026
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14 changes: 11 additions & 3 deletions containers/message-parser/app/default_schemas/extended.json
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Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,7 @@
"reference_lookup": "Bundle.entry.resource.where(resourceType = 'Composition').encounter.reference"
},
"reason_for_visit": {
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition' ).section.where(code.coding.code='29299-5').extension.where(url='http://hl7.org/fhir/cda/ccda/StructureDefinition/2.16.840.1.113883.10.20.22.2.12').valueString",
"fhir_path": "Bundle.entry.resource.where(resourceType= 'Composition' ).section.where(code.coding.code='29299-5').text.`div`",
"data_type": "string",
"nullable": true
},
Expand Down Expand Up @@ -298,8 +298,12 @@
"nullable": true
},
"specimen_type": {
"fhir_path": "Observation.extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Specimen' and id = %ref).type.coding.display",
"data_type": "string",
"reference_lookup": [
"Observation.id",
"Bundle.entry.resource.where(resourceType = 'DiagnosticReport').where(result.where(reference.endsWith(%ref)).exists()).specimen.reference"
],
"nullable": true
},
"performing_lab": {
Expand All @@ -308,8 +312,12 @@
"nullable": true
},
"specimen_collection_date": {
"fhir_path": "Observation.extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"fhir_path": "Bundle.entry.resource.where(resourceType = 'Specimen' and id = %ref).collection.collectedPeriod.start | Bundle.entry.resource.where(resourceType = 'Specimen' and id = %ref).collection.collectedDateTime",
"data_type": "datetime",
"reference_lookup": [
"Observation.id",
"Bundle.entry.resource.where(resourceType = 'DiagnosticReport').where(result.where(reference.endsWith(%ref)).exists()).specimen.reference"
],
"nullable": true
}
}
Expand Down
9 changes: 4 additions & 5 deletions containers/message-parser/app/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -446,11 +446,10 @@ def _get_reference(self, field_parser, current_message):
curr_ref = fhirpathpy.evaluate(message, ref_parser)

if len(curr_ref) == 0:
self.response.status_code = status.HTTP_400_BAD_REQUEST
raise ValueError(
"Provided `reference_lookup` location does not point to a "
"referencing identifier"
)
# No matching reference was found. Treat as missing data and
# propagate an empty reference so the downstream lookup resolves to
# a null value instead of failing the entire parse.
curr_ref.append("")
# Future refactor: Each reference_parser can only refer to one reference
elif len(curr_ref) > 1:
self.response.status_code = status.HTTP_400_BAD_REQUEST
Expand Down