Merge branch 'main' into gordon/refactor-rr-info-parsing

.github/workflows/container-fhir-converter.yaml

@@ -94,18 +94,6 @@ jobs:
         working-directory: ./containers/${{env.CONTAINER}}/tests/integration
         run: |
           python -m pytest -m "integration"
-  unit-test-dotnet-fhir-converter:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-      - name: Setup dotnet
-        uses: actions/setup-dotnet@v3
-        with:
-          dotnet-version: "8.0.x"
-      - name: Run tests
-        working-directory: ./containers/${{env.CONTAINER}}
-        run: dotnet test
   build-container:
     runs-on: ubuntu-latest
     steps:

containers/ecr-viewer/seed-scripts/create-seed-data.py

@@ -1,3 +1,4 @@
+import argparse
 import json
 import os
 import traceback
@@ -8,7 +9,22 @@
 BASEDIR = os.path.dirname(os.path.abspath(__file__))
 
 
-def convert_files():
+def _get_args():
+    parser = argparse.ArgumentParser(
+        prog="Create Seed Data",
+        description="Convert eICR and RR files to FHIR bundles and insert them into the database.",
+        epilog="For each directory in baseECR/LA the script will look for a `CDA_eICR.xml` and `CDA_RR.xml` file. If they are found, it will convert them into a FHIR bundle (saved as `bundle.json`) and insert that into the database using the Orchestration service.",
+    )
+    parser.add_argument(
+        "-s",
+        "--skip_convert",
+        action="store_true",
+        help="If this is set, if `bundle.json` already exists, the script will not look for `CDA_eICR.xml` and `CDA_RR.xml` files to convert them again, and use the existing `bundle.json`.",
+    )
+    return parser.parse_args()
+
+
+def _process_files(args):
     """
     Convert eICR and RR into FHIR bundles using the FHIR converter.
 
@@ -28,7 +44,24 @@ def convert_files():
 
                 # Check if it's a directory
                 if os.path.isdir(folder_path):
-                    try:
+                    # If `bundle.json` exists and ski_convert is set just upload the bundle
+                    if (
+                        os.path.exists(os.path.join(folder_path, "bundle.json"))
+                        and args.skip_convert
+                    ):
+                        # Just upload the bundle
+                        with open(
+                            os.path.join(folder_path, "bundle.json")
+                        ) as fhir_file:
+                            payload = {
+                                "message_type": "fhir",
+                                "data_type": "fhir",
+                                "config_file_name": "save-bundle-to-ecr-viewer.json",
+                                "message": json.load(fhir_file),
+                            }
+                            _process_eicrs(subfolder, folder, folder_path, payload)
+                    # If we are not just inserting the bundle, check for the necessary files
+                    elif os.path.exists(os.path.join(folder_path, "CDA_eICR.xml")):
                         # Open the necessary files in the folder
                         with (
                             open(
@@ -41,49 +74,52 @@ def convert_files():
                             payload = {
                                 "message_type": "ecr",
                                 "data_type": "ecr",
-                                "config_file_name": "seed-ecr-viewer-config.json",
+                                "config_file_name": "save-eicr-to-ecr-viewer-config.json",
                                 "message": eicr_file.read(),
                                 "rr_data": rr_file.read(),
                             }
-
-                            print(f"{URL}/process-message for {subfolder}/{folder}")
-
-                            response = requests.post(
-                                f"{URL}/process-message", json=payload
-                            )
-                            if response.status_code == 200:
-                                responses_json = response.json()["processed_values"][
-                                    "responses"
-                                ]
-                                for response in responses_json:
-                                    if "stamped_ecr" in response:
-                                        with open(
-                                            os.path.join(folder_path, "bundle.json"),
-                                            "w",
-                                        ) as fhir_file:
-                                            json.dump(
-                                                response["stamped_ecr"][
-                                                    "extended_bundle"
-                                                ],
-                                                fhir_file,
-                                                indent=4,
-                                            )
-                                print(
-                                    f"Converted {folder} in {subfolder} successfully."
-                                )
-                            # Handle the case where the response fails
-                            else:
-                                print(f"Failed to convert {folder} in {subfolder}.")
-                    # Handle file not found or other potential errors
-                    except FileNotFoundError as e:
-                        print(f"Required file not found in {folder_path}: {e}")
-                    except Exception as e:
+                            _process_eicrs(subfolder, folder, folder_path, payload)
+                    # If neither `bundle.json` nor `CDA_eICR.xml` exists, skip processing
+                    else:
                         print(
-                            f"An error occurred processing {folder} in {subfolder}: {e}\n\n{traceback.format_exc()}"
+                            f"Neither `bundle.json` nor `CDA_eICR.xml` found in {folder_path}. Skipping."
                         )
+                        continue
+
                 # If the subfolder is not a directory, print a message
                 else:
                     print(f"{subfolder_path} is not a valid directory.")
 
 
-convert_files()
+def _process_eicrs(subfolder, folder, folder_path, payload):
+    try:
+        print(f"{URL}/process-message for {subfolder}/{folder}")
+        response = requests.post(f"{URL}/process-message", json=payload)
+        if response.status_code == 200:
+            responses_json = response.json()["processed_values"]["responses"]
+            for response in responses_json:
+                if "stamped_ecr" in response:
+                    with open(
+                        os.path.join(folder_path, "bundle.json"), "w"
+                    ) as fhir_file:
+                        json.dump(
+                            response["stamped_ecr"]["extended_bundle"],
+                            fhir_file,
+                            indent=4,
+                        )
+            print(f"Converted {folder} in {subfolder} successfully.")
+        # Handle the case where the response fails
+        else:
+            print(f"Failed to convert {folder} in {subfolder}.")
+    # Handle file not found or other potential errors
+    except FileNotFoundError as e:
+        print(f"Required file not found in {folder_path}: {e}")
+    except Exception as e:
+        print(
+            f"An error occurred processing {folder} in {subfolder}: {e}\n\n{traceback.format_exc()}"
+        )
+
+
+if __name__ == "__main__":
+    args = _get_args()
+    _process_files(args)

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/components/EcrPaginationWrapper.tsx

@@ -104,7 +104,6 @@ const EcrPaginationWrapper = ({
             }}
           >
             <React.Fragment>
-              <option value="6">6</option>
               <option value="25">25</option>
               <option value="50">50</option>
               <option value="75">75</option>

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

@@ -129,15 +129,9 @@ export const evaluatePatientContactInfo = (
   fhirBundle: Bundle,
   mappings: PathMappings,
 ) => {
-  const phoneNumbers = evaluate(fhirBundle, mappings.patientPhoneNumbers)
-    .map(
-      (phoneNumber) =>
-        `${
-          phoneNumber?.use?.charAt(0).toUpperCase() +
-          phoneNumber?.use?.substring(1)
-        } ${phoneNumber.value}`,
-    )
-    .join("\n");
+  const phoneNumbers = formatContactPoint(
+    evaluate(fhirBundle, mappings.patientPhoneNumbers),
+  ).join("\n");
   const emails = evaluate(fhirBundle, mappings.patientEmails)
     .map((email) => `${email.value}`)
     .join("\n");

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;
@@ -211,19 +211,24 @@ export const formatDate = (dateString?: string): string | undefined => {
   }
 };
 
+const VALID_PHONE_NUMBER_REGEX = /^\d{3}-\d{3}-\d{4}$/;
 /**
  * Formats a phone number into a standard format of XXX-XXX-XXXX.
  * @param phoneNumber - The phone number to format.
- * @returns The formatted phone number or undefined if the input is invalid.
+ * @returns The formatted phone number or "Invalid Number" if the input is invalid or undefined if the input is empty.
  */
-export const formatPhoneNumber = (phoneNumber: string) => {
-  try {
-    return phoneNumber
-      .replace("+1", "")
-      .replace(/\D/g, "")
-      .replace(/(\d{3})(\d{3})(\d{4})/, "$1-$2-$3");
-  } catch {
-    return undefined;
+export const formatPhoneNumber = (phoneNumber: string): string | undefined => {
+  if (!phoneNumber || phoneNumber.trim() === "") return undefined;
+
+  const formatted = phoneNumber
+    .replace("+1", "")
+    .replace(/\D/g, "")
+    .replace(/(\d{3})(\d{3})(\d{4})/, "$1-$2-$3");
+
+  if (VALID_PHONE_NUMBER_REGEX.test(formatted)) {
+    return formatted;
+  } else {
+    return "Invalid Number";
   }
 };
 
@@ -481,7 +486,7 @@ function processTable(table: Element): TableRow[] {
 }
 
 function getElementContent(el: Node): string {
-  return sanitizeHtml(el.textContent?.trim() ?? "");
+  return sanitizeAndMap(el.textContent?.trim() ?? "");
 }
 
 /**
@@ -508,31 +513,6 @@ export function extractNumbersAndPeriods(inputValues: string[]): string[] {
   });
 }
 
-/**
- * Truncates up to the character limit. If it stops in the middle of the word, it removes the whole word.
- * @param input_str - The string to truncate
- * @param character_limit - The number of characters to truncate defaults to 30
- * @returns - The string that was
- */
-export const truncateLabNameWholeWord = (
-  input_str: string,
-  character_limit: number = 30,
-) => {
-  if (input_str.length <= character_limit) {
-    return input_str;
-  }
-
-  const trimStr = input_str.substring(0, 30);
-  const lastSpaceIndex = trimStr.lastIndexOf(" ");
-
-  if (lastSpaceIndex === -1) {
-    return input_str.length <= character_limit ? input_str : "";
-  }
-
-  // Truncate to the last full word within the limit
-  return input_str.substring(0, lastSpaceIndex);
-};
-
 /**
  * Converts a string to sentence case, making the first character uppercase and the rest lowercase.
  * @param str - The string to convert to sentence case.
@@ -596,11 +576,18 @@ export const formatContactPoint = (
       const phoneNumberUse = toSentenceCase(contactPoint.use ?? "");
       contactArr.push(
         [phoneNumberUse, formatPhoneNumber(contactPoint.value ?? "")]
-          .join(" ")
-          .trim(),
+          .filter((c) => c)
+          .join(": "),
       );
     } else if (contactPoint.system === "email" && contactPoint.value) {
       contactArr.push(contactPoint.value);
+    } else if (contactPoint.system === "fax" && contactPoint.value) {
+      const faxNumberUse = toSentenceCase(contactPoint.use ?? "");
+      contactArr.push(
+        [faxNumberUse, "Fax:", formatPhoneNumber(contactPoint.value ?? "")]
+          .join(" ")
+          .trim(),
+      );
     }
   }
   return contactArr;

containers/ecr-viewer/src/app/tests/components/EcrPaginationWrapper.test.tsx

@@ -143,4 +143,19 @@ describe("Pagination for EcrPaginationWrapper", () => {
 
     expect(screen.getByText("Showing 0-0 of 0 eCRs")).toBeInTheDocument();
   });
+
+  it("the dropdown should only have 25, 50, 75, and 100 as options", async () => {
+    render(
+      <EcrPaginationWrapper totalCount={0}>
+        <br />
+      </EcrPaginationWrapper>,
+    );
+
+    const select = screen.getByTestId("Select");
+    expect(select.children).toHaveLength(4);
+    expect(select.children[0]).toHaveTextContent("25");
+    expect(select.children[1]).toHaveTextContent("50");
+    expect(select.children[2]).toHaveTextContent("75");
+    expect(select.children[3]).toHaveTextContent("100");
+  });
 });

containers/ecr-viewer/src/app/tests/components/__snapshots__/EcrPaginationWrapper.test.tsx.snap

@@ -149,11 +149,6 @@ exports[`EcrPaginationWrapper should match snapshot 1`] = `
           id="input-select"
           name="input-select"
         >
-          <option
-            value="6"
-          >
-            6
-          </option>
           <option
             value="25"
           >

containers/ecr-viewer/src/app/tests/components/__snapshots__/LabInfo.test.tsx.snap

@@ -14,10 +14,9 @@ exports[`LabInfo should match snapshot test 1`] = `
         <div>
           <h4
             class="usa-summary-box__heading padding-y-105"
-            id="lab-results-from-providence-st-joseph-medical"
+            id="lab-results-from-providence-st-joseph-medical-center-laboratory-clia-05d0672675"
           >
-            Lab Results from 
-                PROVIDENCE ST. JOSEPH MEDICAL
+            Lab Results from PROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
           </h4>
           <div
             class="usa-summary-box__text"
@@ -782,8 +781,7 @@ Burbank, CA
             class="usa-summary-box__heading padding-y-105"
             id="lab-results-from-vumc-cerner-lab"
           >
-            Lab Results from 
-                VUMC CERNER LAB
+            Lab Results from VUMC CERNER LAB
           </h4>
           <div
             class="usa-summary-box__text"