Add alcohol use, intake, and comment (#3043)

* init * Add alcohol use, intake, and comment. * remove bad change * Update to evaluateValue * pr comments * PR comment * Fix ? to && * Upgrade fhir-converter to v18 * update snap * one last snap update * ugh * fix integration test * change to correct release * update to next release * Fix orch pin multipart * update fastapi * undo * increase timeout * revert snap
CDCgov · Dec 17, 2024 · 8a4842b · 8a4842b
1 parent 744ea3f
commit 8a4842b
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Showing 7 changed files with 228 additions and 5 deletions.
diff --git a/containers/ecr-viewer/src/app/api/fhirPath.yml b/containers/ecr-viewer/src/app/api/fhirPath.yml
@@ -21,7 +21,9 @@ patientCurrentJobTitle: "Bundle.entry.resource.where(resourceType='Observation')
 patientTobaccoUse: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='72166-2').where(category.coding.code='social-history').value"
 patientHomelessStatus: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='75274-1').where(category.coding.code='social-history').value"
 patientPregnancyStatus: "Bundle.entry.resource.where(resourceType='Observation').where(meta.profile='http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-pregnancy-status-observation').value"
-patientAlcoholUse: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='11331-6').where(category.coding.code='social-history').value"
+patientAlcoholUse: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.where(code='11331-6' and system = 'http://loinc.org')).value"
+patientAlcoholIntake: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.where(code='74013-4' and system = 'http://loinc.org')).value"
+patientAlcoholComment: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.display='Alcohol Comment').value"
 patientSexualOrientation: "Bundle.entry.resource.where(resourceType='Observation').where(code.coding.code='76690-7').value"
 patientGenderIdentity: "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http://hl7.org/fhir/us/ecr/StructureDefinition/us-ph-genderidentity-extension').value"
 patientReligion: "Bundle.entry.resource.where(resourceType = 'Patient').extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-religion').value"

diff --git a/containers/ecr-viewer/src/app/services/evaluateFhirDataService.ts b/containers/ecr-viewer/src/app/services/evaluateFhirDataService.ts
@@ -31,6 +31,7 @@ import { DisplayDataProps } from "@/app/view-data/components/DataDisplay";
 import { evaluateTravelHistoryTable } from "./socialHistoryService";
 import { Path } from "fhirpath";
 import { returnTableFromJson } from "../view-data/components/common";
+import { toSentenceCase } from "./formatService";
 
 /**
  * Evaluates patient name from the FHIR bundle and formats it into structured data for display.
@@ -197,6 +198,39 @@ export const calculatePatientAgeAtDeath = (
   }
 };
 
+/**
+ * Evaluates alcohol use information from the FHIR bundle and formats it into structured data for display.
+ * @param fhirBundle - The FHIR bundle containing alcohol use data.
+ * @param fhirMappings - The object containing the fhir paths.
+ * @returns An array of evaluated and formatted alcohol use data.
+ */
+export const evaluateAlcoholUse = (
+  fhirBundle: Bundle,
+  fhirMappings: PathMappings,
+) => {
+  const alcoholUse = evaluateValue(fhirBundle, fhirMappings.patientAlcoholUse);
+  const alcoholIntake = evaluateValue(
+    fhirBundle,
+    fhirMappings.patientAlcoholIntake,
+  );
+  let alcoholComment: string | undefined = evaluateValue(
+    fhirBundle,
+    fhirMappings.patientAlcoholComment,
+  );
+
+  if (alcoholComment) {
+    alcoholComment = toSentenceCase(alcoholComment);
+  }
+
+  return [
+    alcoholUse ? `Use: ${alcoholUse}` : null,
+    alcoholIntake ? `Intake (standard drinks/week): ${alcoholIntake}` : null,
+    alcoholComment ? `Comment: ${alcoholComment}` : null,
+  ]
+    .filter(Boolean) // Removes null or undefined lines
+    .join("\n"); // Joins the remaining lines with newlines
+};
+
 /**
  * Evaluates social data from the FHIR bundle and formats it into structured data for display.
  * @param fhirBundle - The FHIR bundle containing social data.
@@ -227,7 +261,7 @@ export const evaluateSocialData = (
     },
     {
       title: "Alcohol Use",
-      value: evaluateValue(fhirBundle, mappings["patientAlcoholUse"]),
+      value: evaluateAlcoholUse(fhirBundle, mappings),
     },
     {
       title: "Sexual Orientation",

diff --git a/containers/ecr-viewer/src/app/tests/assets/BundlePatient.json b/containers/ecr-viewer/src/app/tests/assets/BundlePatient.json
@@ -177,6 +177,171 @@
         "method": "PUT",
         "url": "Patient/6b6b3c4c-4884-4a96-b6ab-c46406839cea"
       }
+    },
+    {
+      "fullUrl": "urn:uuid:b91cab75-e4a0-2227-79ec-44c9c8ea795a",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "b91cab75-e4a0-2227-79ec-44c9c8ea795a",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"
+          ],
+          "source": "ecr"
+        },
+        "identifier": [
+          {
+            "system": "urn:oid:1.2.840.114350.1.13.66.2.7.7.698084.19222",
+            "value": "Z13909121"
+          }
+        ],
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "social-history"
+              }
+            ]
+          }
+        ],
+        "status": "final",
+        "code": {
+          "coding": [
+            {
+              "code": "X-SDOH-19222",
+              "system": "urn:oid:1.2.840.114350.1.72.1.8",
+              "display": "Alcohol Comment"
+            }
+          ]
+        },
+        "effectiveDateTime": "2022-11-04",
+        "valueString": "1-2 DRINKS 2 TO 4 TIMES A MONTH",
+        "subject": {
+          "reference": "Patient/5227f761-a6ea-461d-9523-8d9ee26eab84"
+        }
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Observation/b91cab75-e4a0-2227-79ec-44c9c8ea795a"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:259df789-9da2-9b7c-bc69-a60c634860d8",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "259df789-9da2-9b7c-bc69-a60c634860d8",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"
+          ],
+          "source": "ecr"
+        },
+        "identifier": [
+          {
+            "system": "urn:oid:1.2.840.114350.1.13.66.2.7.1.1040.13",
+            "value": "Z13909121^54660.98^897148007"
+          }
+        ],
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "social-history"
+              }
+            ]
+          }
+        ],
+        "status": "final",
+        "code": {
+          "coding": [
+            {
+              "code": "897148007",
+              "system": "http://snomed.info/sct",
+              "display": "Alcoholic beverage intake"
+            },
+            {
+              "code": "74013-4",
+              "system": "http://loinc.org",
+              "display": "Alcoholic drinks per day"
+            }
+          ]
+        },
+        "effectiveDateTime": "2024-01-31",
+        "valueQuantity": {
+          "value": ".29",
+          "unit": "/d"
+        },
+        "subject": {
+          "reference": "Patient/5227f761-a6ea-461d-9523-8d9ee26eab84"
+        }
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Observation/259df789-9da2-9b7c-bc69-a60c634860d8"
+      }
+    },
+    {
+      "fullUrl": "urn:uuid:b467f663-f4f5-78af-a677-05b5545d8716",
+      "resource": {
+        "resourceType": "Observation",
+        "id": "b467f663-f4f5-78af-a677-05b5545d8716",
+        "meta": {
+          "profile": [
+            "http://hl7.org/fhir/us/core/StructureDefinition/us-core-observationresults"
+          ],
+          "source": "ecr"
+        },
+        "identifier": [
+          {
+            "system": "urn:oid:1.2.840.114350.1.13.66.2.7.1.1040.12",
+            "value": "Z13909121^54660.98^897148007"
+          }
+        ],
+        "category": [
+          {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/observation-category",
+                "code": "social-history"
+              }
+            ]
+          }
+        ],
+        "status": "final",
+        "code": {
+          "coding": [
+            {
+              "code": "897148007",
+              "system": "http://snomed.info/sct",
+              "display": "Alcoholic beverage intake"
+            },
+            {
+              "code": "11331-6",
+              "system": "http://loinc.org",
+              "display": "History of Alcohol Use"
+            }
+          ]
+        },
+        "effectiveDateTime": "2024-01-31",
+        "valueCodeableConcept": {
+          "coding": [
+            {
+              "code": "219006",
+              "system": "http://snomed.info/sct",
+              "display": "Current drinker of alcohol (finding)"
+            }
+          ]
+        },
+        "subject": {
+          "reference": "Patient/5227f761-a6ea-461d-9523-8d9ee26eab84"
+        }
+      },
+      "request": {
+        "method": "PUT",
+        "url": "Observation/b467f663-f4f5-78af-a677-05b5545d8716"
+      }
     }
   ]
 }
diff --git a/containers/ecr-viewer/src/app/tests/services/evaluateFhirDataServices.test.ts b/containers/ecr-viewer/src/app/tests/services/evaluateFhirDataServices.test.ts
@@ -12,6 +12,7 @@ import {
   evaluatePatientName,
   evaluateDemographicsData,
   evaluateEncounterCareTeamTable,
+  evaluateAlcoholUse,
 } from "@/app/services/evaluateFhirDataService";
 import { Bundle, Patient } from "fhir/r4";
 import BundleWithMiscNotes from "@/app/tests/assets/BundleMiscNotes.json";
@@ -516,3 +517,24 @@ describe("Evaluate Patient Name", () => {
     expect(actual).toEqual("ABEL CASTILLO");
   });
 });
+
+describe("Evaluate Alcohol Use", () => {
+  it("should return the use, intake comment", () => {
+    const actual = evaluateAlcoholUse(
+      BundleWithPatient as unknown as Bundle,
+      mappings,
+    );
+    expect(actual).toEqual(
+      "Use: Current drinker of alcohol (finding)\n" +
+        "Intake (standard drinks/week): .29/d\n" +
+        "Comment: 1-2 drinks 2 to 4 times a month",
+    );
+  });
+  it("should empty string because there is no use, intake, or comment", () => {
+    const actual = evaluateAlcoholUse(
+      BundlePatientMultiple as unknown as Bundle,
+      mappings,
+    );
+    expect(actual).toEqual("");
+  });
+});
diff --git a/containers/fhir-converter/Dockerfile b/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-17 --single-branch /build/FHIR-Converter
+RUN git clone https://github.com/skylight-hq/FHIR-Converter.git --branch v7.0-skylight-18 --single-branch /build/FHIR-Converter
 
 WORKDIR /build/FHIR-Converter
 

diff --git a/containers/orchestration/tests/integration/test_orchestration.py b/containers/orchestration/tests/integration/test_orchestration.py
@@ -148,7 +148,7 @@ def test_failed_save_to_ecr_viewer(setup, clean_up_db):
         }
         files = {"upload_file": ("file.zip", file)}
         orchestration_response = httpx.post(
-            PROCESS_ZIP_ENDPOINT, data=form_data, files=files, timeout=60
+            PROCESS_ZIP_ENDPOINT, data=form_data, files=files, timeout=120
         )
         assert orchestration_response.status_code == 500
 

diff --git a/poetry.lock b/poetry.lock