Fix ordering of notes/comments (#2900)

* fix: move things to fhir converter, unify make and docker * ci: remove dotnet testing * fix: undo debugging docker changes * fix: more debugging clenaup * docs: update README with current dev guidance and pointing to the fork * feat: allow passing the converter tool path as an environment variable * fix: rename environment variable * fix: point to converter pr * fix: sanitize and map the incoming original inner tex * test: add unit tests * fix: use valueString when available * test: update snapshot * docs: add section header comment * test: update snapshot * test: more snapshot updating * fix: gender identity fhirpath, parsing lab notes * fix: point to corresponding FHIR-Converter branch * fix: update to v7.0-skylight-7 release * refactor: move selection logic into fhirpath * fix: escape div * test: make sure tests cover the changes * Update containers/fhir-converter/Dockerfile
CDCgov · Nov 15, 2024 · 6e86ee7 · 6e86ee7
1 parent 86b63e1
commit 6e86ee7
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Showing 8 changed files with 17 additions and 14 deletions.
diff --git a/containers/ecr-viewer/src/app/api/fhirPath.yml b/containers/ecr-viewer/src/app/api/fhirPath.yml
@@ -89,17 +89,16 @@ activeProblemsDisplay: "Condition.code.coding.display.first()"
 activeProblemsOnsetDate: "Condition.onsetDateTime"
 activeProblemsOnsetAge: "Condition.onsetAge.value"
 activeProblemsComments: "Condition.note[0].text"
-historyOfPresentIllness: "Bundle.entry.resource.where(resourceType = 'Composition').section.where(code.coding.code = '10164-2').text"
+historyOfPresentIllness: "Bundle.entry.resource.where(resourceType = 'Composition').section.where(code.coding.code = '10164-2').text.`div`.first()"
 
 # Treatment Details
-planOfTreatment: "Bundle.entry.resource.section.where(title = 'Plan of Treatment').text"
+planOfTreatment: "Bundle.entry.resource.section.where(title = 'Plan of Treatment').text.first().`div`"
 plannedProcedures: "Bundle.entry.resource.where(resourceType = 'CarePlan').activity"
 plannedProcedureName: "detail.code.coding[0].display"
 plannedProcedureOrderedDate: "extension.where(url = 'dibbs.orderedDate').valueString"
 plannedProcedureScheduledDate: "detail.scheduledString"
 
 # Administered Medications
-administeredMedications: "Bundle.entry.resource.section.where(code.coding[0].code = '29549-3').text"
 adminMedicationsRefs: "Bundle.entry.resource.section.where(code.coding[0].code = '29549-3').entry.reference"
 
 ## Care Team
@@ -126,7 +125,7 @@ procedureReason: "Procedure.reason.display"
 # Lab Info
 diagnosticReports: "Bundle.entry.resource.where(resourceType = 'DiagnosticReport')"
 observations: "Bundle.entry.resource.where(resourceType = 'Observation')"
-labResultDiv: "Bundle.entry.resource.section.where(code.coding[0].code = '30954-2').text"
+labResultDiv: "Bundle.entry.resource.section.where(code.coding[0].code = '30954-2').text.`div`.first()"
 specimenCollectionTime: "Observation.extension[0].extension.where(url = 'specimen collection time').valueDateTime"
 specimenReceivedTime: "Observation.extension[0].extension.where(url = 'specimen receive time').valueDateTime"
 specimenSource: "Observation.extension[0].extension.where(url = 'specimen source').valueString"

diff --git a/containers/ecr-viewer/src/app/services/labsService.tsx b/containers/ecr-viewer/src/app/services/labsService.tsx
@@ -88,7 +88,7 @@ export const getLabJsonObject = (
   const observationRefVal = [...new Set(observationRefValsArray)].join(", "); // should only be 1
 
   // Get lab reports HTML String (for all lab reports) & convert to JSON
-  const labsString = evaluate(fhirBundle, mappings["labResultDiv"])[0].div;
+  const labsString = evaluateValue(fhirBundle, mappings["labResultDiv"]);
   const labsJson = formatTablesToJSON(labsString);
 
   // Get specified lab report (by reference value)
@@ -341,7 +341,7 @@ export const evaluateDiagnosticReportData = (
       infoPath: "observationDeviceReference",
       applyToValue: (ref) => {
         const device = evaluateReference(fhirBundle, mappings, ref) as Device;
-        return device.deviceName?.[0]?.name;
+        return parse(sanitizeAndMap(device.deviceName?.[0]?.name ?? ""));
       },
       className: "minw-10 width-20",
     },

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundleLab.json b/containers/ecr-viewer/src/app/tests/assets/BundleLab.json
@@ -792,7 +792,7 @@
         "valueString": "Acinetobacter baumannii",
         "note": [
           {
-            "text": "Lab comment"
+            "text": "<paragraph>Lab comment</paragraph>"
           }
         ],
         "effectiveDateTime": "2022-04-18T19:57:02Z",

diff --git a/containers/ecr-viewer/src/app/tests/components/__snapshots__/LabInfo.test.tsx.snap b/containers/ecr-viewer/src/app/tests/components/__snapshots__/LabInfo.test.tsx.snap
@@ -988,7 +988,9 @@ NASHVILLE, TN
                         class="hideableData p-list"
                         colspan="5"
                       >
-                        Lab comment
+                        <p>
+                          Lab comment
+                        </p>
                       </td>
                     </tr>
                   </tbody>

diff --git a/containers/ecr-viewer/src/app/view-data/components/common.tsx b/containers/ecr-viewer/src/app/view-data/components/common.tsx
@@ -1,6 +1,7 @@
 import {
   calculatePatientAge,
   evaluateReference,
+  evaluateValue,
 } from "@/app/services/evaluateFhirDataService";
 import EvaluateTable, {
   BuildHeaders,
@@ -255,8 +256,8 @@ export const returnPlanOfTreatmentContent = (
   fhirBundle: Bundle,
   mappings: PathMappings,
 ) => {
-  const bundle = evaluate(fhirBundle, mappings["planOfTreatment"]);
-  const rawTables = formatTablesToJSON(bundle[0]?.div);
+  const bundle = evaluateValue(fhirBundle, mappings["planOfTreatment"]);
+  const rawTables = formatTablesToJSON(bundle);
   const tables = rawTables
     .map((rawTable) => returnPlanOfTreatmentTable(rawTable))
     .filter((t) => !!t);
@@ -500,7 +501,7 @@ export const evaluateClinicalData = (
       title: "Miscellaneous Notes",
       value: parse(
         sanitizeAndMap(
-          evaluate(fhirBundle, mappings["historyOfPresentIllness"])[0]?.div,
+          evaluateValue(fhirBundle, mappings["historyOfPresentIllness"]),
         ) || "",
       ),
     },

diff --git a/containers/fhir-converter/Dockerfile b/containers/fhir-converter/Dockerfile
@@ -1,7 +1,7 @@
 FROM mcr.microsoft.com/dotnet/sdk:6.0 AS build
 
 # Download FHIR-Converter
-RUN git clone https://github.com/skylight-hq/FHIR-Converter.git --branch v7.0-skylight-7 --single-branch /build/FHIR-Converter
+RUN git clone https://github.com/skylight-hq/FHIR-Converter.git --branch v7.0-skylight-8 --single-branch /build/FHIR-Converter
 
 WORKDIR /build/FHIR-Converter
 

diff --git a/containers/fhir-converter/tests/integration/__snapshots__/test_FHIR-Converter.ambr b/containers/fhir-converter/tests/integration/__snapshots__/test_FHIR-Converter.ambr
@@ -7543,7 +7543,7 @@
             }),
             'note': list([
               dict({
-                'text': '<paragraph styleCode="xcellHeader" xmlns="urn:hl7-org:v3">Last Assessment &amp; Plan: </paragraph><content xmlns="urn:hl7-org:v3"><content styleCode="xLabel">Formatting of this note might be different from the original.</content><br />This is my note about this problem.</content><br xmlns="urn:hl7-org:v3" />',
+                'text': '<content xmlns="urn:hl7-org:v3">A note:</content><paragraph styleCode="xcellHeader" xmlns="urn:hl7-org:v3">Last Assessment &amp; Plan: </paragraph><content xmlns="urn:hl7-org:v3"><content styleCode="xLabel">Formatting of this note might be different from the original.</content><br />This is my note about this problem.</content><br xmlns="urn:hl7-org:v3" />',
               }),
             ]),
             'onsetDateTime': '2019-04-16',

diff --git a/...hir-converter/tests/test_files/snapshot/f3eae968-d262-40f1-b1cb-699dda5b395a/CDA_eICR.xml b/...hir-converter/tests/test_files/snapshot/f3eae968-d262-40f1-b1cb-699dda5b395a/CDA_eICR.xml
@@ -769,6 +769,7 @@
                                 </tr>
                                 <tr styleCode="xRowAlt xMergeUp">
                                     <td ID="problem14comment" colspan="2" styleCode="xallIndent">
+                                        <content>A note:</content>
                                         <paragraph styleCode="xcellHeader">Last Assessment &amp;
                                             Plan: </paragraph>
                                         <content><content styleCode="xLabel">Formatting of this note
@@ -5784,4 +5785,4 @@
             </component>
         </structuredBody>
     </component>
-</ClinicalDocument>
+</ClinicalDocument>