Correct FHIR produced by TCRS (#3093)

* Correct FHIR produced by TCRS * Fix tests * Missed a test * Another test * Update test bundles
CDCgov · Jan 3, 2025 · 9f705c7 · 9f705c7
1 parent 6f59c59
commit 9f705c7
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Showing 11 changed files with 89 additions and 141 deletions.
diff --git a/containers/ecr-viewer/src/app/services/ecrSummaryService.tsx b/containers/ecr-viewer/src/app/services/ecrSummaryService.tsx
@@ -1,4 +1,10 @@
-import { Address, Bundle, Condition, Extension, Observation } from "fhir/r4";
+import {
+  Address,
+  Bundle,
+  Condition,
+  DiagnosticReport,
+  Observation,
+} from "fhir/r4";
 import { evaluateData, PathMappings } from "@/app/view-data/utils/utils";
 import {
   formatAddress,
@@ -13,39 +19,10 @@ import {
 } from "./evaluateFhirDataService";
 import { DisplayDataProps } from "@/app/view-data/components/DataDisplay";
 import { returnProblemsTable } from "@/app/view-data/components/common";
-import {
-  LabReport,
-  evaluateLabInfoData,
-  isLabReportElementDataList,
-} from "./labsService";
+import { evaluateLabInfoData, isLabReportElementDataList } from "./labsService";
 import { ConditionSummary } from "@/app/view-data/components/EcrSummary";
 import React from "react";
 
-/**
- * ExtensionConditionCode extends the FHIR Extension interface to include a 'coding' property.
- * This property aligns with the CDC's ReportStream specifications for condition
- * to code mappings, using 'coding.code' for descriptive names of testing methods.
- *
- * Refer to the ReportStream documentation for details:
- * https://github.com/CDCgov/prime-reportstream/blob/master/prime-router/docs/design/0023-condition-to-code-mapping.md
- */
-interface ExtensionConditionCode extends Extension {
-  coding?: { code: string; system: string }[];
-}
-
-interface ConditionStamped extends Condition {
-  extension?: ExtensionConditionCode[];
-}
-
-interface LabReportStamped extends LabReport {
-  id: string;
-  extension?: ExtensionConditionCode[];
-}
-
-interface ObservationStamped extends Observation {
-  extension?: ExtensionConditionCode[];
-}
-
 /**
  * Evaluates and retrieves patient details from the FHIR bundle using the provided path mappings.
  * @param fhirBundle - The FHIR bundle containing patient data.
@@ -266,7 +243,7 @@ export const evaluateEcrSummaryRelevantClinicalDetails = (
     return [{ value: noData, dividerLine: true }];
   }
 
-  const problemsList: ConditionStamped[] = evaluate(
+  const problemsList: Condition[] = evaluate(
     fhirBundle,
     fhirPathMappings["activeProblems"],
   );
@@ -275,7 +252,7 @@ export const evaluateEcrSummaryRelevantClinicalDetails = (
       (ext) =>
         ext.url ===
           "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code" &&
-        ext.coding?.some((item) => item.code === snomedCode),
+        ext.valueCoding?.code === snomedCode,
     ),
   );
 
@@ -313,7 +290,7 @@ export const evaluateEcrSummaryRelevantLabResults = (
     return [{ value: noData, dividerLine: true }];
   }
 
-  const labReports: LabReportStamped[] = evaluate(
+  const labReports: DiagnosticReport[] = evaluate(
     fhirBundle,
     fhirPathMappings["diagnosticReports"],
   );
@@ -322,22 +299,19 @@ export const evaluateEcrSummaryRelevantLabResults = (
       (ext) =>
         ext.url ===
           "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code" &&
-        ext.coding?.some((item) => item.code === snomedCode),
+        ext.valueCoding?.code === snomedCode,
     ),
   );
 
   const obsIdsWithCode: (string | undefined)[] = (
-    evaluate(
-      fhirBundle,
-      fhirPathMappings["observations"],
-    ) as ObservationStamped[]
+    evaluate(fhirBundle, fhirPathMappings["observations"]) as Observation[]
   )
     .filter((entry) =>
       entry.extension?.some(
         (ext) =>
           ext.url ===
             "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code" &&
-          ext.coding?.some((item) => item.code === snomedCode),
+          ext.valueCoding?.code === snomedCode,
       ),
     )
     .map((entry) => entry.id);
@@ -351,7 +325,7 @@ export const evaluateEcrSummaryRelevantLabResults = (
         return false;
       }
 
-      return lab.result.some((result) => {
+      return lab.result?.some((result) => {
         if (result.reference) {
           const referenceId = result.reference.replace(/^Observation\//, "");
           return obsIds.has(referenceId);

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundleClinicalInfo.json b/containers/ecr-viewer/src/app/tests/assets/BundleClinicalInfo.json
@@ -883,12 +883,10 @@
         "extension": [
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "263133002",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "263133002",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "onsetDateTime": "2019-04-16",

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundleEcrSummary.json b/containers/ecr-viewer/src/app/tests/assets/BundleEcrSummary.json
@@ -495,12 +495,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "performer": [
@@ -566,12 +564,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "50711007",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "50711007",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "performer": [
@@ -640,12 +636,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "performer": [
@@ -795,12 +789,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "subject": {
@@ -1016,12 +1008,10 @@
         "extension": [
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ]
       },

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundleLab.json b/containers/ecr-viewer/src/app/tests/assets/BundleLab.json
@@ -555,12 +555,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "test-snomed",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "test-snomed",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "subject": {
@@ -912,12 +910,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "test-snomed",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "test-snomed",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "subject": {

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundleLabInvalidResultsDiv.json b/containers/ecr-viewer/src/app/tests/assets/BundleLabInvalidResultsDiv.json
@@ -327,12 +327,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "test-snomed",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "test-snomed",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "subject": {

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundleLabNoLabIds.json b/containers/ecr-viewer/src/app/tests/assets/BundleLabNoLabIds.json
@@ -849,12 +849,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "performer": [
@@ -951,12 +949,10 @@
           },
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ],
         "performer": [
@@ -1380,12 +1376,10 @@
         "extension": [
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ]
       },
@@ -1450,12 +1444,10 @@
         "extension": [
           {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [
-              {
-                "code": "840539006",
-                "system": "http://snomed.info/sct"
-              }
-            ]
+            "valueCoding": {
+              "code": "840539006",
+              "system": "http://snomed.info/sct"
+            }
           }
         ]
       },

diff --git a/containers/trigger-code-reference/app/utils.py b/containers/trigger-code-reference/app/utils.py
@@ -222,7 +222,7 @@ def add_code_extension_and_human_readable_name(resource: dict, code: str) -> dic
     resource["extension"].append(
         {
             "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-            "coding": [{"code": code, "system": "http://snomed.info/sct"}],
+            "valueCoding": {"code": code, "system": "http://snomed.info/sct"},
         }
     )
 

diff --git a/containers/trigger-code-reference/assets/sample_stamp_condition_extensions_responses.json b/containers/trigger-code-reference/assets/sample_stamp_condition_extensions_responses.json
@@ -60,12 +60,10 @@
                       },
                       {
                         "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-                        "coding": [
-                          {
-                            "code": "840539006",
-                            "system": "http://snomed.info/sct"
-                          }
-                        ]
+                        "valueCoding": {
+                          "code": "840539006",
+                          "system": "http://snomed.info/sct"
+                        }
                       }
                     ],
                     "performer": [
@@ -378,12 +376,10 @@
                     "extension": [
                       {
                         "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-                        "coding": [
-                          {
-                            "code": "840539006",
-                            "system": "http://snomed.info/sct"
-                          }
-                        ]
+                        "valueCoding": {
+                          "code": "840539006",
+                          "system": "http://snomed.info/sct"
+                        }
                       }
                     ],
                     "request": {

diff --git a/containers/trigger-code-reference/tests/integration/test_trigger_code_reference.py b/containers/trigger-code-reference/tests/integration/test_trigger_code_reference.py
@@ -46,12 +46,10 @@ def test_tcr_stamping(setup, fhir_bundle):
         for ext in extensions:
             if ext == {
                 "url": "https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code",
-                "coding": [
-                    {
-                        "code": reportable_condition_code,
-                        "system": "http://snomed.info/sct",
-                    }
-                ],
+                "valueCoding": {
+                    "code": reportable_condition_code,
+                    "system": "http://snomed.info/sct",
+                },
             }:
                 stamped_resources.append(resource.get("id"))
                 break