fix: Add lookup of rxnorm codes to names, return all codes provided (#…

…2816) * fix: Add lookup of rxnorm codes to names, return all codes provided * fix: tell build about rxnorm.csv * build: try using a user to get curl to work * build: a different incantation * build: install jq in the docker container * fix: handle multiple medication codes in the front end * [pre-commit.ci] auto fixes from pre-commit hooks * test: add unit tests for getMedicationDisplayName * fix: export getMedicationDisplayName for testing * [pre-commit.ci] auto fixes from pre-commit hooks * test: test medication conversion * fix: handle observation data change * [pre-commit.ci] auto fixes from pre-commit hooks * test: more lab results * fix: pr feedback * fix: handle null codes * fix: change unknown to unknown medication name * docs: more debugging hints * fix: handle null pointer * fix: more robust coding name check --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
CDCgov · Oct 29, 2024 · 98a4eed · 98a4eed
1 parent e3abfe5
commit 98a4eed
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Showing 21 changed files with 123,624 additions and 92 deletions.
diff --git a/containers/ecr-viewer/src/app/api/fhirPath.yml b/containers/ecr-viewer/src/app/api/fhirPath.yml
@@ -134,14 +134,14 @@ specimenCollectionTime: "Observation.extension[0].extension.where(url = 'specime
 specimenReceivedTime: "Observation.extension[0].extension.where(url = 'specimen receive time').valueDateTime"
 specimenSource: "Observation.extension[0].extension.where(url = 'specimen source').valueString"
 observationReferenceValue: "Observation.extension[0].extension.where(url = 'observation entry reference value').valueString"
-observationComponent: "code.coding.display"
+observationComponent: "code.coding.display.first()"
 observationValue: (valueQuantity.value.toString() | valueString | iif(interpretation.coding.display.exists(), ' (' | interpretation.coding.display | ')', '')).join('')
 observationReferenceRange: "referenceRange.text"
 observationDeviceReference: "device.reference"
 observationNote: "note.text"
 observationMethod: "method"
-observationOrganism: "code.coding.display"
-observationAntibiotic: "code.coding.display"
+observationOrganism: "code.coding.display.first()"
+observationAntibiotic: "code.coding.display.first()"
 observationOrganismMethod: "extension.where(url = 'methodCode originalText').valueString"
 observationSusceptibility: "valueString"
 

diff --git a/containers/ecr-viewer/src/app/services/labsService.tsx b/containers/ecr-viewer/src/app/services/labsService.tsx
@@ -11,7 +11,7 @@ import {
   formatPhoneNumber,
   TableJson,
 } from "@/app/services/formatService";
-import { ObservationComponent } from "fhir/r4b";
+import { Coding, ObservationComponent } from "fhir/r4b";
 import EvaluateTable, {
   ColumnInfoInput,
 } from "@/app/view-data/components/EvaluateTable";
@@ -284,7 +284,8 @@ export function evaluateObservationTable(
     ) ?? []
   ).filter(
     (observation) =>
-      !observation.component && observation.code?.coding[0]?.display,
+      !observation.component &&
+      observation.code?.coding.some((c: Coding) => c?.display),
   );
 
   let obsTable;
@@ -521,7 +522,7 @@ export const evaluateLabInfoData = (
     const element = (
       <AccordionLabResults
         key={report.id}
-        title={report.code.coding[0].display}
+        title={report.code.coding.find((c: Coding) => c.display).display}
         abnormalTag={checkAbnormalTag(labReportJson)}
         content={content}
         organizationId={organizationId}

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundleLab.json b/containers/ecr-viewer/src/app/tests/assets/BundleLab.json
@@ -290,10 +290,19 @@
         "status": "final",
         "code": {
           "coding": [
+            {
+              "code": "somelocalcode",
+              "system": "some.thing"
+            },
             {
               "code": "LAB10082",
               "display": "STOOL PATHOGENS, NAAT, 12 TO 25 TARGETS",
               "system": "http://www.ama-assn.org/go/cpt"
+            },
+            {
+              "code": "a loinc code",
+              "display": "Stool Pathogens 12 To 25 Targets",
+              "system": "http://loinc.org"
             }
           ]
         },
@@ -412,6 +421,10 @@
         "status": "final",
         "code": {
           "coding": [
+            {
+              "code": "somelocalcode",
+              "system": "1.2.3"
+            },
             {
               "code": "82196-7",
               "display": "Campylobacter, NAAT",

diff --git a/containers/ecr-viewer/src/app/tests/view-data.test.tsx b/containers/ecr-viewer/src/app/tests/view-data.test.tsx
@@ -1,6 +1,7 @@
 import React from "react";
 import { render } from "@testing-library/react";
 import ECRViewerPage from "../view-data/page";
+import { getMedicationDisplayName } from "../view-data/components/common";
 
 jest.mock("../view-data/component-utils", () => ({
   metrics: jest.fn(),
@@ -34,3 +35,62 @@ describe("ECRViewerPage", () => {
     unmount(); // Clean up
   });
 });
+
+describe("getMedicationDisplayName", () => {
+  it("handles undefined case", () => {
+    expect(getMedicationDisplayName(undefined)).toBe(undefined);
+  });
+
+  it("handles empty case", () => {
+    expect(getMedicationDisplayName({ coding: [] })).toBe(undefined);
+  });
+
+  it("handles single named case", () => {
+    expect(
+      getMedicationDisplayName({
+        coding: [{ code: "123", display: "medication", system: "ABC" }],
+      }),
+    ).toBe("medication");
+  });
+
+  it("handles single un-named case", () => {
+    expect(
+      getMedicationDisplayName({
+        coding: [{ code: "123", system: "ABC" }],
+      }),
+    ).toBe("Unknown medication name - ABC code 123");
+  });
+
+  it("handles multiple named case", () => {
+    expect(
+      getMedicationDisplayName({
+        coding: [
+          { code: "123", display: "first", system: "ABC" },
+          { code: "456", display: "second", system: "DEF" },
+        ],
+      }),
+    ).toBe("first");
+  });
+
+  it("handles multiple mixed named case", () => {
+    expect(
+      getMedicationDisplayName({
+        coding: [
+          { code: "123", system: "ABC" },
+          { code: "456", display: "second", system: "DEF" },
+        ],
+      }),
+    ).toBe("second");
+  });
+
+  it("handles multiple un-named case", () => {
+    expect(
+      getMedicationDisplayName({
+        coding: [
+          { code: "123", system: "ABC" },
+          { code: "456", system: "DEF" },
+        ],
+      }),
+    ).toBe("Unknown medication name - ABC code 123");
+  });
+});
diff --git a/containers/ecr-viewer/src/app/view-data/components/AdministeredMedication.tsx b/containers/ecr-viewer/src/app/view-data/components/AdministeredMedication.tsx
@@ -9,7 +9,7 @@ type AdministeredMedicationProps = {
   medicationData: AdministeredMedicationTableData[];
 };
 export type AdministeredMedicationTableData = {
-  name: string;
+  name?: string;
   date?: string;
 };
 

diff --git a/containers/ecr-viewer/src/app/view-data/components/common.tsx b/containers/ecr-viewer/src/app/view-data/components/common.tsx
@@ -25,6 +25,7 @@ import {
   Bundle,
   CarePlanActivity,
   CareTeamParticipant,
+  CodeableConcept,
   Condition,
   FhirResource,
   Immunization,
@@ -661,16 +662,42 @@ const evaluateAdministeredMedication = (
         );
       }
 
-      if (medication?.code?.coding?.[0]?.display) {
-        data.push({
-          date:
-            medicationAdministration.effectiveDateTime ??
-            medicationAdministration.effectivePeriod?.start,
-          name: medication?.code?.coding?.[0]?.display,
-        });
-      }
+      data.push({
+        date:
+          medicationAdministration.effectiveDateTime ??
+          medicationAdministration.effectivePeriod?.start,
+        name: getMedicationDisplayName(medication?.code),
+      });
       return data;
     },
     [],
   );
 };
+
+/**
+ * Given a CodeableConcept, find an appropriate display name
+ * @param code - The codable concept if available.
+ * @returns - String with a name to display (can be "Unknown")
+ */
+export function getMedicationDisplayName(
+  code: CodeableConcept | undefined,
+): string | undefined {
+  const codings = code?.coding ?? [];
+  let name;
+  // Pull out the first name we find,
+  for (const coding of codings) {
+    if (coding.display) {
+      name = coding.display;
+      break;
+    }
+  }
+
+  // There is a code, but no names, pull out the first code to give the user
+  // something to go off of
+  if (name === undefined && codings.length > 0) {
+    const { system, code } = codings[0];
+    name = `Unknown medication name - ${system} code ${code}`;
+  }
+
+  return name;
+}
diff --git a/containers/fhir-converter/CustomFhir/CustomFhir.csproj b/containers/fhir-converter/CustomFhir/CustomFhir.csproj
@@ -29,4 +29,10 @@
     </Content>
   </ItemGroup>
 
-</Project>
+  <ItemGroup>
+    <Content Include="rxnorm.csv">
+      <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
+    </Content>
+  </ItemGroup>
+
+</Project>
diff --git a/containers/fhir-converter/CustomFhir/CustomFilters.cs b/containers/fhir-converter/CustomFhir/CustomFilters.cs
@@ -7,6 +7,7 @@
 using Newtonsoft.Json.Linq;
 using Microsoft.VisualBasic.FileIO;
 using DotLiquid.Util;
+using System.IO.Enumeration;
 
 namespace Microsoft.Health.Fhir.Liquid.Converter
 {
@@ -22,6 +23,7 @@ public partial class Filters
         {"paragraph", "p"}
     };
     private static Dictionary<string, string>? loincDict;
+    private static Dictionary<string, string>? rxnormDict;
 
     // Items from the filter could be arrays or objects, process them to be the same
     private static List<Dictionary<string, object>> ProcessItem(object item)
@@ -306,9 +308,9 @@ private static string CleanStringFromTabs(string value)
     // Overloaded method with default level value
     public static void PrintObject(object obj)
     {
-      var devMode = Environment.GetEnvironmentVariable("DEV_MODE");
-      var debugLog = Environment.GetEnvironmentVariable("DEBUG_LOG");
-      if (devMode != "true" || debugLog != "true")
+      var devMode = Environment.GetEnvironmentVariable("DEV_MODE") ?? "false";
+      var debugLog = Environment.GetEnvironmentVariable("DEBUG_LOG") ?? "false";
+      if (devMode.Trim() != "true" || debugLog.Trim() != "true")
       {
         return;
       }
@@ -318,9 +320,9 @@ public static void PrintObject(object obj)
 
     private static void PrintObject(object obj, int level)
     {
-      var devMode = Environment.GetEnvironmentVariable("DEV_MODE");
-      var debugLog = Environment.GetEnvironmentVariable("DEBUG_LOG");
-      if (devMode != "true" || debugLog != "true")
+      var devMode = Environment.GetEnvironmentVariable("DEV_MODE") ?? "false";
+      var debugLog = Environment.GetEnvironmentVariable("DEBUG_LOG") ?? "false";
+      if (devMode.Trim() != "true" || debugLog.Trim() != "true")
       {
         return;
       }
@@ -455,12 +457,12 @@ public static string ToHtmlStringJoinBr(object data)
     }
 
     /// <summary>
-    /// Parses a CSV file containing LOINC codes and Long Common Names and returns a dictionary where the LOINC codes are keys and the LCN are values.
+    /// Parses a CSV file containing keys and values in the first and second columns and returns a dictionary.
     /// </summary>
-    /// <returns>A dictionary where the keys are LOINC codes and the values are descriptions.</returns>
-    private static Dictionary<string, string> LoincDictionary()
+    /// <returns>A dictionary where the keys are codes and the values are descriptions.</returns>
+    private static Dictionary<string, string> CSVMapDictionary(string filename)
     {
-      TextFieldParser parser = new TextFieldParser("Loinc.csv");
+      TextFieldParser parser = new TextFieldParser(filename);
       Dictionary<string, string> csvData = new Dictionary<string, string>();
 
       parser.HasFieldsEnclosedInQuotes = true;
@@ -489,8 +491,20 @@ private static Dictionary<string, string> LoincDictionary()
     /// <returns>The name associated with the specified LOINC code, or null if the code is not found in the dictionary.</returns>
     public static string? GetLoincName(string loinc)
     {
-      loincDict ??= LoincDictionary();
-      loincDict.TryGetValue(loinc, out string? element);
+      loincDict ??= CSVMapDictionary("Loinc.csv");
+      loincDict.TryGetValue(loinc ?? string.Empty, out string? element);
+      return element;
+    }
+
+    /// <summary>
+    /// Retrieves the name associated with the specified RxNorm code from the RxNorm dictionary.
+    /// </summary>
+    /// <param name="rxnorm">The RxNorm code for which to retrieve the name.</param>
+    /// <returns>The name associated with the specified LOINC code, or null if the code is not found in the dictionary.</returns>
+    public static string? GetRxnormName(string rxnorm)
+    {
+      rxnormDict ??= CSVMapDictionary("rxnorm.csv");
+      rxnormDict.TryGetValue(rxnorm ?? string.Empty, out string? element);
       return element;
     }
 
@@ -714,4 +728,4 @@ public static IDictionary<string, bool> GetDiagnosisDictionary(IList<object> ent
       return result;
     }
   }
-}
+}
diff --git a/containers/fhir-converter/CustomFhir/CustomFiltersTests.cs b/containers/fhir-converter/CustomFhir/CustomFiltersTests.cs
@@ -183,6 +183,36 @@ public void GetLoincName_InvalidLOINC_ReturnsNull()
     var actual = Filters.GetLoincName(loinc);
     Assert.Null(actual);
   }
+
+  [Fact]
+  public void GetLoincName_Null_ReturnsNull()
+  {
+    var actual = Filters.GetLoincName(null);
+    Assert.Null(actual);
+  }
+
+  [Fact]
+  public void GetRxnormName_ValidRxnorm_ReturnsName()
+  {
+    var rxnorm = "1044916";
+    var actual = Filters.GetRxnormName(rxnorm);
+    Assert.Equal("VioNex", actual);
+  }
+
+  [Fact]
+  public void GetRxnormName_InvalidRxnorm_ReturnsNull()
+  {
+    var rxnorm = "ABC";
+    var actual = Filters.GetRxnormName(rxnorm);
+    Assert.Null(actual);
+  }
+
+  [Fact]
+  public void GetRxnormName_Null_ReturnsNull()
+  {
+    var actual = Filters.GetRxnormName(null);
+    Assert.Null(actual);
+  }
 
   [Fact]
   public void FindObjectByIdRecursive_ValidId_ReturnsObject()
@@ -296,4 +326,4 @@ public void GetDiagnosisDictionary_ReturnsDiagnosisDictionary()
     var actual = Filters.GetDiagnosisDictionary(CustomFilterTestFixtures.EncounterDiagnoses);
     Assert.Equal(new Dictionary<string, bool>() {{ "B05.9", true }, { "B06.0", true }, { "B06.1", true }}, actual);
   }
-}
+}