fix: handle more problem note formats (#2866)

* 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

* Update containers/fhir-converter/Dockerfile

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

@@ -84,7 +84,7 @@ resolve: "Bundle.entry.resource.where(resourceType = %resourceType).where(id = %
 
 # Clinical Info
 activeProblems: "Bundle.entry.resource.where(resourceType='Condition').where(category.coding.code='problem-item-list')"
-activeProblemsDisplay: "Condition.code.coding[0].display"
+activeProblemsDisplay: "Condition.code.coding.display.first()"
 activeProblemsOnsetDate: "Condition.onsetDateTime"
 activeProblemsOnsetAge: "Condition.onsetAge.value"
 activeProblemsComments: "Condition.note[0].text"

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

@@ -1,7 +1,7 @@
 import React from "react";
 import { ToolTipElement } from "@/app/view-data/components/ToolTipElement";
 import { ContactPoint } from "fhir/r4";
-import sanitizeHtml from "sanitize-html";
+import { sanitizeAndMap } from "../view-data/utils/utils";
 
 interface Metadata {
   [key: string]: string;
@@ -486,7 +486,7 @@ function processTable(table: Element): TableRow[] {
 }
 
 function getElementContent(el: Node): string {
-  return sanitizeHtml(el.textContent?.trim() ?? "");
+  return sanitizeAndMap(el.textContent?.trim() ?? "");
 }
 
 /**

containers/ecr-viewer/src/app/tests/utils.test.tsx

@@ -1,4 +1,4 @@
-import { isDataAvailable } from "@/app/view-data/utils/utils";
+import { isDataAvailable, sanitizeAndMap } from "@/app/view-data/utils/utils";
 import { loadYamlConfig } from "@/app/api/utils";
 import { Bundle } from "fhir/r4";
 import BundleWithTravelHistory from "./assets/BundleTravelHistory.json";
@@ -550,4 +550,20 @@ describe("Utils", () => {
       expect(tip.className).not.toInclude("short-tooltip");
     });
   });
+
+  describe("sanitizeAndMap", () => {
+    it("should leave alone nice safe HTML", () => {
+      const html = "<p>hi there</p>";
+      const actual = sanitizeAndMap(html);
+      expect(actual).toBe(html);
+    });
+
+    it("should map xml-y HTML", () => {
+      const html = `<paragraph>hi there</paragraph><content ID="abc">I'm content</content><list><item>one</item><item>two</item></list>`;
+      const actual = sanitizeAndMap(html);
+      expect(actual).toBe(
+        `<p>hi there</p><span>I'm content</span><ul><li>one</li><li>two</li></ul>`,
+      );
+    });
+  });
 });

containers/ecr-viewer/src/app/view-data/components/EvaluateTable.tsx

@@ -168,7 +168,7 @@ const BuildRow: React.FC<BuildRowProps> = ({
       hiddenRows.push(
         <tr hidden={hiddenComment} id={`hidden-comment-${index}`}>
           <td colSpan={columns.length} className={"hideableData p-list"}>
-            {splitStringWith(`${rowCellData}`, "<br>")}
+            {rowCellData}
           </td>
         </tr>,
       );

containers/ecr-viewer/src/app/view-data/components/common.tsx

@@ -21,12 +21,14 @@ import {
   PathMappings,
   evaluateData,
   noData,
+  sanitizeAndMap,
 } from "@/app/view-data/utils/utils";
 import {
   Bundle,
   CarePlanActivity,
   CareTeamParticipant,
   CodeableConcept,
+  Coding,
   Condition,
   FhirResource,
   Immunization,
@@ -38,7 +40,6 @@ import {
 } from "fhir/r4";
 import { evaluate } from "@/app/view-data/utils/evaluate";
 import parse from "html-react-parser";
-import sanitizeHtml from "sanitize-html";
 import { DisplayDataProps } from "@/app/view-data/components/DataDisplay";
 import {
   AdministeredMedication,
@@ -192,8 +193,8 @@ export const returnProblemsTable = (
   problemsArray: Condition[],
   mappings: PathMappings,
 ): React.JSX.Element | undefined => {
-  problemsArray = problemsArray.filter(
-    (entry) => entry.code?.coding?.[0].display,
+  problemsArray = problemsArray.filter((entry) =>
+    entry.code?.coding?.some((c: Coding) => c?.display),
   );
 
   if (problemsArray.length === 0) {
@@ -210,6 +211,7 @@ export const returnProblemsTable = (
     {
       columnName: "Comments",
       infoPath: "activeProblemsComments",
+      applyToValue: (v) => parse(sanitizeAndMap(v)),
       hiddenBaseText: "comment",
     },
   ];
@@ -497,7 +499,7 @@ export const evaluateClinicalData = (
     {
       title: "Miscellaneous Notes",
       value: parse(
-        sanitizeHtml(
+        sanitizeAndMap(
           evaluate(fhirBundle, mappings["historyOfPresentIllness"])[0]?.div,
         ) || "",
       ),

containers/ecr-viewer/src/app/view-data/utils/utils.tsx

@@ -1,6 +1,7 @@
 import React from "react";
 import { removeHtmlElements } from "@/app/services/formatService";
 import { DisplayDataProps } from "@/app/view-data/components/DataDisplay";
+import sanitizeHtml from "sanitize-html";
 
 export interface PathMappings {
   [key: string]: string;
@@ -57,3 +58,19 @@ export const isDataAvailable = (item: DisplayDataProps): Boolean => {
   }
   return true;
 };
+
+/**
+ * Sanitizes the html while also mapping common hl7v3 tags to html.
+ * @param val - The string of content to sanitize and map.
+ * @returns - Returns sanitized and mapped content.
+ */
+export const sanitizeAndMap = (val: string): string => {
+  return sanitizeHtml(val, {
+    transformTags: {
+      paragraph: "p",
+      list: "ul",
+      item: "li",
+      content: "span",
+    },
+  });
+};

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-3 --single-branch /build/FHIR-Converter
+RUN git clone https://github.com/skylight-hq/FHIR-Converter.git --branch v7.0-skylight-4 --single-branch /build/FHIR-Converter
 
 WORKDIR /build/FHIR-Converter