Map single entry symptom responses to FHIR #8183

emyl3 · 2024-10-10T16:43:00Z

BACKEND PULL REQUEST

Related Issue

Resolves Send symptoms from single entry AOE form to ReportStream #6609

Changes Proposed

Maps single entry symptom responses to FHIR to match the format described here

{
    "fullUrl": "Observation/12345",
    "resource": {
        "resourceType": "Observation",
        "id": "12345",
        "identifier": [
            {
                "use": "official",
                "type": {
                    "coding": [
                        {
                            "system": "http://loinc.org/",
                            "code": "99582-9",
                            "display": "Symptom and timing panel"
                        }
                    ]
                }
            }
        ],
        "status": "final",
        "code": {
            "coding": [
                {
                    "system": "http://loinc.org/",
                    "code": "75325-1",
                    "display": "Symptom"
                }
            ],
            "text": "Symptom"
        },
        "subject": {
            "reference": "Patient/12345"
        },
        "valueCodeableConcept": {
            "coding": [
                {
                    "system": "http://snomed.info/sct",
                    "code": "111516008",
                    "display": "Blurred vision"
                }
            ]
        }
    }
}

Additional Information

N/A

Testing

elisa/log-6609-symptoms-fhir-single-entry branch has been pushed so you can see a log in your backend console with the symptoms mapped to FHIR

emyl3 · 2024-10-10T17:24:39Z

backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java

@@ -802,7 +807,7 @@ private void addCorrectionNote(
    }
  }

-  public Set<Observation> convertToAOESymptomObservation(
+  public Set<Observation> convertToAOESymptomaticObservation(


⚠️ renamed it to be more accurate with the observation we are adding

emyl3 · 2024-10-10T17:38:24Z

backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConstants.java

@@ -51,6 +51,8 @@ private FhirConstants() {

  public static final String LOINC_AOE_IDENTIFIER = "81959-9";
  public static final String LOINC_AOE_SYMPTOMATIC = "95419-8";
+  public static final String LOINC_SYMPTOM_TIMING_PANEL = "99582-9";


⚠️ https://loinc.org/99582-9/

emyl3 · 2024-10-10T17:38:59Z

backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConstants.java

@@ -51,6 +51,8 @@ private FhirConstants() {

  public static final String LOINC_AOE_IDENTIFIER = "81959-9";
  public static final String LOINC_AOE_SYMPTOMATIC = "95419-8";
+  public static final String LOINC_SYMPTOM_TIMING_PANEL = "99582-9";
+  public static final String LOINC_SYMPTOM = "75325-1";


⚠️ https://loinc.org/75325-1/

emyl3 · 2024-10-10T17:50:04Z

backend/src/main/java/gov/cdc/usds/simplereport/api/Translators.java

@@ -378,6 +378,51 @@ public static String parseState(String s) {
    throw IllegalGraphqlArgumentException.invalidInput(s, "state");
  }

+  private static final Map<String, String> RESPIRATORY_SYMPTOMS =


⚠️ symptoms taken from this frontend file

separated them out like the frontend -- thought this would make things easier to read and consistent with the frontend

Let me know if you all prefer one map of these symptoms

This logic makes sense to me, especially considering that it's how we are making the distinction between symptoms across the rest of the app.

bobbywells52 · 2024-10-11T16:57:00Z

backend/src/main/java/gov/cdc/usds/simplereport/api/converter/FhirConverter.java

+      List<String> positiveSymptoms = getPositiveSymptoms(surveyData.getSymptoms());
+      observations.addAll(convertToSymptomsObservations(positiveSymptoms));


This is very clean and makes sense to me from a logic perspective. However, does anyone know why we weren't making the distinction between postive and negative symptoms before in the Fhir conversion?

Or was that distinction already being made, just without the helper function?

We were only adding the "Yes" symptomatic observation if there were true symptom values (see line 973 above)

Since that only checks if any symptom value is true, I needed to create an additional method to return all the symptoms that were true so it's easier to create an Observation for each positive symptom.

Let me know if that makes sense or you see any other optimization! 😸

I think this is a tiny bit unclear - I would have initially assumed Positive and Negative meant that it was a positive or negative test result.

I'll rename this and the variable... maybe something like trueSymptoms and getTrueSymptoms
edit: ended up renaming it as getFilteredTrueSymptoms

Ok I updated this! Let me know if that makes it more clear! 😸

Small nit for the name, I think symptomsPresent and getFilteredSymptomsPresent would be clearer than "true" and be consistent with the clinical context of patients presenting with certain symptoms

Thank you for the suggestion! I like those better! Naming is hard 😅

bobbywells52

Left some clarifying questions for myself but overall looks great! Thanks for your work on this

mpbrown

LGTM testing it out locally! Great work on this!

DanielSass

Overall this looks good. Left one comment on a piece I think could be more clear.

sonarqubecloud · 2024-10-23T18:57:27Z

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
98.5% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

mpbrown

🚢

emyl3 commented Oct 10, 2024

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emyl3 force-pushed the elisa/6609-symptoms-fhir-single-entry branch 2 times, most recently from bb0be5d to fa1b9b9 Compare October 10, 2024 18:56

emyl3 temporarily deployed to dev2 October 10, 2024 20:37 — with GitHub Actions Inactive

Map single entry symptom responses to FHIR

5f7623b

emyl3 force-pushed the elisa/6609-symptoms-fhir-single-entry branch from fa1b9b9 to 5f7623b Compare October 10, 2024 20:51

emyl3 temporarily deployed to dev2 October 10, 2024 20:58 — with GitHub Actions Inactive

emyl3 temporarily deployed to dev2 October 10, 2024 21:06 — with GitHub Actions Inactive

emyl3 temporarily deployed to dev2 October 10, 2024 21:09 — with GitHub Actions Inactive

emyl3 marked this pull request as ready for review October 10, 2024 21:19

emyl3 requested review from mehansen, DanielSass, mpbrown and bobbywells52 October 10, 2024 21:19

bobbywells52 reviewed Oct 11, 2024

View reviewed changes

bobbywells52 previously approved these changes Oct 11, 2024

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mpbrown previously approved these changes Oct 15, 2024

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DanielSass previously approved these changes Oct 16, 2024

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Rename method and variable

4703aa6

emyl3 dismissed stale reviews from DanielSass, mpbrown, and bobbywells52 via 4703aa6 October 21, 2024 18:56

emyl3 requested review from DanielSass, mpbrown and bobbywells52 October 21, 2024 22:24

emyl3 temporarily deployed to dev3 October 22, 2024 14:51 — with GitHub Actions Inactive

emyl3 temporarily deployed to dev3 October 22, 2024 14:58 — with GitHub Actions Inactive

emyl3 temporarily deployed to dev3 October 22, 2024 15:01 — with GitHub Actions Inactive

bobbywells52 previously approved these changes Oct 22, 2024

View reviewed changes

Rename method and variable

233a041

emyl3 dismissed bobbywells52’s stale review via 233a041 October 23, 2024 18:39

emyl3 requested a review from bobbywells52 October 23, 2024 18:39

mpbrown approved these changes Oct 24, 2024

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DanielSass approved these changes Oct 24, 2024

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emyl3 added this pull request to the merge queue Oct 24, 2024

Merged via the queue into main with commit 43f780f Oct 24, 2024
32 checks passed

emyl3 deleted the elisa/6609-symptoms-fhir-single-entry branch October 24, 2024 16:35

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Map single entry symptom responses to FHIR #8183

Map single entry symptom responses to FHIR #8183

emyl3 commented Oct 10, 2024 •

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sonarqubecloud bot commented Oct 23, 2024

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		List<String> positiveSymptoms = getPositiveSymptoms(surveyData.getSymptoms());
		observations.addAll(convertToSymptomsObservations(positiveSymptoms));

Map single entry symptom responses to FHIR #8183

Map single entry symptom responses to FHIR #8183

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emyl3 commented Oct 10, 2024 • edited Loading

BACKEND PULL REQUEST

Related Issue

Changes Proposed

Additional Information

Testing

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sonarqubecloud bot commented Oct 23, 2024

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emyl3 commented Oct 10, 2024 •

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