Merge branch 'main' into boban/2873-env-variables-next-runtime-env

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+# These owners will be the default owners for everything in
+# the repo. Unless a later match takes precedence,
+# they will be requested for review when someone opens a pull request.
+*       @akasper @angelathe @austin-hall-skylight @BobanL @gordonfarrell @JNygaard-Skylight @lina-roth @mcmcgrath13 @robertmitchellv

containers/ecr-viewer/src/app/api/fhirPath.yml

@@ -2,6 +2,7 @@ patientNameList: "Bundle.entry.resource.where(resourceType = 'Patient').name"
 patientAddressList: "Bundle.entry.resource.where(resourceType = 'Patient').address"
 patientTelecom: "Bundle.entry.resource.where(resourceType = 'Patient').telecom"
 patientCounty: "Bundle.entry.resource.where(resourceType = 'Patient').address.first().county"
+patientCountry: "Bundle.entry.resource.where(resourceType = 'Patient').address.first().country"
 
 patientIds: "Bundle.entry.resource.where(resourceType = 'Patient').identifier.where(system != 'urn:ietf:rfc:3986').value.join('\n')"
 patientDOB: "Bundle.entry.resource.where(resourceType = 'Patient').birthDate"
@@ -21,7 +22,9 @@ patientCurrentJobTitle: "Bundle.entry.resource.where(resourceType='Observation')
 patientTobaccoUse: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='72166-2').where(category.coding.code='social-history').value"
 patientHomelessStatus: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='75274-1').where(category.coding.code='social-history').value"
 patientPregnancyStatus: "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-pregnancy-status-observation').value"
-patientAlcoholUse: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='11331-6').where(category.coding.code='social-history').value"
+patientAlcoholUse: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.where(code='11331-6' and system = 'http://loinc.org')).value"
+patientAlcoholIntake: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.where(code='74013-4' and system = 'http://loinc.org')).value"
+patientAlcoholComment: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.display='Alcohol Comment').value"
 patientSexualOrientation: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='76690-7').value"
 patientGenderIdentity: "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-genderidentity-extension').value"
 patientReligion: "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-religion').value"

containers/ecr-viewer/src/app/api/save-fhir-data/save-fhir-data-service.ts

@@ -358,12 +358,20 @@ export const saveMetadataToSqlServer = async (
               sql.VarChar(50),
               lab.test_result_code_system,
             )
-            .input("test_result_interpretation", sql.VarChar(255), null) // Not implemented
-            .input("test_result_interpretation_code", sql.VarChar(50), null) // Not implemented
+            .input(
+              "test_result_interpretation",
+              sql.VarChar(255),
+              lab.test_result_interpretation,
+            )
+            .input(
+              "test_result_interpretation_code",
+              sql.VarChar(50),
+              lab.test_result_interpretation_code,
+            )
             .input(
               "test_result_interpretation_system",
               sql.VarChar(255),
-              lab.test_result_interp_system,
+              lab.test_result_interpretation_system,
             )
             .input(
               "test_result_ref_range_low_value",

containers/ecr-viewer/src/app/api/save-fhir-data/types.ts

@@ -9,7 +9,9 @@ interface Lab {
   test_result_code: string | undefined;
   test_result_code_display: string | undefined;
   test_result_code_system: string | undefined;
-  test_result_interp_system: string | undefined;
+  test_result_interpretation: string | undefined;
+  test_result_interpretation_code: string | undefined;
+  test_result_interpretation_system: string | undefined;
   test_result_ref_range_low: string | undefined;
   test_result_ref_range_low_units: string | undefined;
   test_result_ref_range_high: string | undefined;

containers/ecr-viewer/src/app/services/evaluateFhirDataService.ts

@@ -31,6 +31,7 @@ import { DisplayDataProps } from "@/app/view-data/components/DataDisplay";
 import { evaluateTravelHistoryTable } from "./socialHistoryService";
 import { Path } from "fhirpath";
 import { returnTableFromJson } from "../view-data/components/common";
+import { toSentenceCase } from "./formatService";
 
 /**
  * Evaluates patient name from the FHIR bundle and formats it into structured data for display.
@@ -197,6 +198,39 @@ export const calculatePatientAgeAtDeath = (
   }
 };
 
+/**
+ * Evaluates alcohol use information from the FHIR bundle and formats it into structured data for display.
+ * @param fhirBundle - The FHIR bundle containing alcohol use data.
+ * @param fhirMappings - The object containing the fhir paths.
+ * @returns An array of evaluated and formatted alcohol use data.
+ */
+export const evaluateAlcoholUse = (
+  fhirBundle: Bundle,
+  fhirMappings: PathMappings,
+) => {
+  const alcoholUse = evaluateValue(fhirBundle, fhirMappings.patientAlcoholUse);
+  const alcoholIntake = evaluateValue(
+    fhirBundle,
+    fhirMappings.patientAlcoholIntake,
+  );
+  let alcoholComment: string | undefined = evaluateValue(
+    fhirBundle,
+    fhirMappings.patientAlcoholComment,
+  );
+
+  if (alcoholComment) {
+    alcoholComment = toSentenceCase(alcoholComment);
+  }
+
+  return [
+    alcoholUse ? `Use: ${alcoholUse}` : null,
+    alcoholIntake ? `Intake (standard drinks/week): ${alcoholIntake}` : null,
+    alcoholComment ? `Comment: ${alcoholComment}` : null,
+  ]
+    .filter(Boolean) // Removes null or undefined lines
+    .join("\n"); // Joins the remaining lines with newlines
+};
+
 /**
  * Evaluates social data from the FHIR bundle and formats it into structured data for display.
  * @param fhirBundle - The FHIR bundle containing social data.
@@ -227,7 +261,7 @@ export const evaluateSocialData = (
     },
     {
       title: "Alcohol Use",
-      value: evaluateValue(fhirBundle, mappings["patientAlcoholUse"]),
+      value: evaluateAlcoholUse(fhirBundle, mappings),
     },
     {
       title: "Sexual Orientation",
@@ -313,6 +347,10 @@ export const evaluateDemographicsData = (
       title: "County",
       value: evaluate(fhirBundle, mappings.patientCounty)[0],
     },
+    {
+      title: "Country",
+      value: evaluate(fhirBundle, mappings.patientCountry)[0],
+    },
     {
       title: "Contact",
       value: formatContactPoint(evaluate(fhirBundle, mappings.patientTelecom)),

containers/ecr-viewer/src/app/services/labsService.tsx

@@ -332,7 +332,11 @@ export function evaluateObservationTable(
   ).filter(
     (observation) =>
       !observation.component &&
-      observation.code?.coding.some((c: Coding) => c?.display),
+      // Make sure there is a component name, but it isn't "Lab Interpretation" as that's handled
+      // via the tab on the result's name
+      observation.code?.coding.some(
+        (c: Coding) => c?.display && c?.display !== "Lab Interpretation",
+      ),
   );
 
   let obsTable;

containers/ecr-viewer/src/app/tests/assets/BundleLab.json

@@ -83,6 +83,10 @@
               {
                 "display": "Organism ID",
                 "reference": "Observation/2a4f8fb5-f957-3c30-1353-a30aa441a12b"
+              },
+              {
+                "reference": "Observation/e9c8e4b3-3fec-4f29-a5c5-e45f96680a4c",
+                "display": "Lab Interpretation"
               }
             ]
           }
@@ -265,6 +269,9 @@
           {
             "reference": "Observation/1c0f3367-0588-c90e-fed0-0d8c15c5ac1b"
           },
+          {
+            "reference": "Observation/e9c8e4b3-3fec-4f29-a5c5-e45f96680a4c"
+          },
           {
             "reference": "Observation/ab1ecbd4-6de0-4f78-cea6-a880a15e88bb"
           }
@@ -396,6 +403,73 @@
         "url": "DiagnosticReport/b0f590a6-4bf5-7add-9716-2bd3ba6defb2"
       }
     },
+    {
+      "fullUrl": "urn:uuid:e9c8e4b3-3fec-4f29-a5c5-e45f96680a4c",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "e9c8e4b3-3fec-4f29-a5c5-e45f96680a4c",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"
+          ],
+          "source": "ecr"
+        },
+        "identifier": [
+          {
+            "system": "urn:oid:1.2.840.114350.1.13.202.3.7.2.798268",
+            "value": "476858944"
+          }
+        ],
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "laboratory"
+              }
+            ]
+          }
+        ],
+        "status": "final",
+        "code": {
+          "coding": [
+            {
+              "code": "56850-1",
+              "system": "http://loinc.org",
+              "display": "Lab Interpretation"
+            }
+          ]
+        },
+        "effectiveDateTime": "2022-09-29T21:13:00Z",
+        "valueString": "Abnormal",
+        "extension": [
+          {
+            "url": "http://hl7.org/fhir/R4/specimen.html",
+            "extension": [
+              {
+                "url": "specimen source",
+                "valueString": "Stool"
+              },
+              {
+                "url": "specimen collection time",
+                "valueDateTime": "2022-09-28T20:51:00Z"
+              },
+              {
+                "url": "specimen receive time",
+                "valueDateTime": "2022-09-28T20:51:36Z"
+              }
+            ]
+          }
+        ],
+        "subject": {
+          "reference": "Patient/1586f68b-1a17-4188-ac0b-82c3cbdbfbda"
+        }
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Observation/e9c8e4b3-3fec-4f29-a5c5-e45f96680a4c"
+      }
+    },
     {
       "fullUrl": "urn:uuid:1c0f3367-0588-c90e-fed0-0d8c15c5ac1b",
       "resource": {