add translation function: vsac --> internal valueset (#41)

Co-authored-by: Rob Mitchell <[email protected]>

query-connector/src/app/constants.ts

@@ -326,6 +326,28 @@ export interface ValueSet {
   concepts: Concept[];
 }
 
+export const DEFAULT_ERSD_VERSION = "3";
+
+type DibbsConceptType = "labs" | "medications" | "conditions";
+export type ErsdConceptType =
+  | "ostc"
+  | "lotc"
+  | "lrtc"
+  | "mrtc"
+  | "dxtc"
+  | "sdtc";
+
+export const ersdToDibbsConceptMap: {
+  [k in ErsdConceptType]: DibbsConceptType;
+} = {
+  ostc: "labs",
+  lotc: "labs",
+  lrtc: "labs",
+  mrtc: "medications",
+  dxtc: "conditions",
+  sdtc: "conditions",
+};
+
 /*
  * The expected type of ValueSets grouped by dibbsConceptType for the purpose of display.
  */

query-connector/src/app/database-service.ts

@@ -1,8 +1,14 @@
 "use server";
 import { Pool, PoolConfig, QueryResultRow } from "pg";
-import { Bundle, OperationOutcome } from "fhir/r4";
+import { Bundle, OperationOutcome, ValueSet as FhirValueSet } from "fhir/r4";
+import {
+  Concept,
+  DEFAULT_ERSD_VERSION,
+  ErsdConceptType,
+  ValueSet,
+  ersdToDibbsConceptMap,
+} from "./constants";
 import { encode } from "base-64";
-import { ValueSet } from "./constants";
 
 const getQuerybyNameSQL = `
 select q.query_name, q.id, qtv.valueset_id, vs.name as valueset_name, vs.version, vs.author as author, vs.type, vs.dibbs_concept_type as dibbs_concept_type, qic.concept_id, qic.include, c.code, c.code_system, c.display 
@@ -166,3 +172,38 @@ export async function getVSACValueSet(
     } as OperationOutcome;
   }
 }
+
+/**
+ * Translates a VSAC FHIR bundle to our internal ValueSet struct
+ * @param fhirValueset - The FHIR ValueSet response from VSAC
+ * @param ersdConceptType - The associated clinical concept type from ERSD
+ * @returns An object of type InternalValueSet
+ */
+export async function translateVSACToInternalValueSet(
+  fhirValueset: FhirValueSet,
+  ersdConceptType: ErsdConceptType,
+) {
+  const id = fhirValueset.id;
+  const version = DEFAULT_ERSD_VERSION;
+
+  const name = fhirValueset.title;
+  const author = fhirValueset.publisher;
+
+  const bundleConceptData = fhirValueset?.compose?.include[0];
+  const system = bundleConceptData?.system;
+  const concepts = bundleConceptData?.concept?.map((fhirConcept) => {
+    return { ...fhirConcept, include: false } as Concept;
+  });
+
+  return {
+    valueSetId: id,
+    valueSetVersion: version,
+    valueSetName: name,
+    author: author,
+    system: system,
+    ersdConceptType: ersdConceptType,
+    dibbsConceptType: ersdToDibbsConceptMap[ersdConceptType],
+    includeValueSet: false,
+    concepts: concepts,
+  } as ValueSet;
+}

query-connector/src/app/tests/assets/VSACValueSet.json

@@ -0,0 +1,174 @@
+{
+  "resourceType": "ValueSet",
+  "id": "2.16.840.1.113762.1.4.1146.170",
+  "meta": {
+    "versionId": "58",
+    "lastUpdated": "2023-12-21T17:43:03.000-05:00",
+    "profile": [
+      "http://hl7.org/fhir/StructureDefinition/shareablevalueset",
+      "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/computable-valueset-cqfm",
+      "http://hl7.org/fhir/us/cqfmeasures/StructureDefinition/publishable-valueset-cqfm"
+    ]
+  },
+  "extension": [
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/valueset-author",
+      "valueContactDetail": {
+        "name": "CSTE Author"
+      }
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/valueset-keyWord",
+      "valueString": "Chlamydia,G_STI,Trigger"
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/resource-lastReviewDate",
+      "valueDate": "2024-06-05"
+    },
+    {
+      "url": "http://hl7.org/fhir/StructureDefinition/valueset-effectiveDate",
+      "valueDate": "2023-06-02"
+    }
+  ],
+  "url": "http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1146.170",
+  "identifier": [
+    {
+      "system": "urn:ietf:rfc:3986",
+      "value": "urn:oid:2.16.840.1.113762.1.4.1146.170"
+    }
+  ],
+  "version": "20230602",
+  "name": "ChlamydiaTrachomatisInfectionOrganismOrSubstanceInLabResults",
+  "title": "Chlamydia trachomatis Infection (Organism or Substance in Lab Results)",
+  "status": "active",
+  "date": "2023-06-02T01:03:51-04:00",
+  "publisher": "CSTE Steward",
+  "jurisdiction": [
+    {
+      "extension": [
+        {
+          "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
+          "valueCode": "unknown"
+        }
+      ]
+    }
+  ],
+  "purpose": "(Clinical Focus: This set of values contains organisms or substances relevant for reporting Chlamydia),(Data Element Scope: Organism names reported in laboratory results),(Inclusion Criteria: Chlamydia trachomatis organism or Chlamydia trachomatis substance),(Exclusion Criteria: antibody substances)",
+  "compose": {
+    "include": [
+      {
+        "system": "http://snomed.info/sct",
+        "concept": [
+          {
+            "code": "115289001",
+            "display": "Chlamydia trachomatis, serotype A (organism)"
+          },
+          {
+            "code": "115290005",
+            "display": "Chlamydia trachomatis, serotype B (organism)"
+          },
+          {
+            "code": "115291009",
+            "display": "Chlamydia trachomatis, serotype Ba (organism)"
+          },
+          {
+            "code": "115292002",
+            "display": "Chlamydia trachomatis, serotype C (organism)"
+          },
+          {
+            "code": "115293007",
+            "display": "Chlamydia trachomatis, serotype D (organism)"
+          },
+          {
+            "code": "115294001",
+            "display": "Chlamydia trachomatis, serotype E (organism)"
+          },
+          {
+            "code": "115295000",
+            "display": "Chlamydia trachomatis, serotype F (organism)"
+          },
+          {
+            "code": "115296004",
+            "display": "Chlamydia trachomatis, serotype I (organism)"
+          },
+          {
+            "code": "115297008",
+            "display": "Chlamydia trachomatis, serotype J (organism)"
+          },
+          {
+            "code": "115298003",
+            "display": "Chlamydia trachomatis, serotype K (organism)"
+          },
+          {
+            "code": "115299006",
+            "display": "Chlamydia trachomatis, serotype L (organism)"
+          },
+          {
+            "code": "115300003",
+            "display": "Chlamydia trachomatis, serotype L1 (organism)"
+          },
+          {
+            "code": "115301004",
+            "display": "Chlamydia trachomatis, serotype L2 (organism)"
+          },
+          {
+            "code": "115318000",
+            "display": "Chlamydia trachomatis, serotype L3 (organism)"
+          },
+          {
+            "code": "115319008",
+            "display": "Chlamydia trachomatis, serotype G (organism)"
+          },
+          {
+            "code": "115328009",
+            "display": "Chlamydia trachomatis, serotype H (organism)"
+          },
+          {
+            "code": "121002007",
+            "display": "Antigen of Chlamydia trachomatis (substance)"
+          },
+          {
+            "code": "121015003",
+            "display": "Antigen of Chlamydia trachomatis serotype F (substance)"
+          },
+          {
+            "code": "121016002",
+            "display": "Antigen of Chlamydia trachomatis serotype G (substance)"
+          },
+          {
+            "code": "121017006",
+            "display": "Antigen of Chlamydia trachomatis serotype K (substance)"
+          },
+          {
+            "code": "121106008",
+            "display": "Ribosomal ribonucleic acid of Chlamydia trachomatis (substance)"
+          },
+          {
+            "code": "121181000",
+            "display": "Deoxyribonucleic acid of Chlamydia trachomatis (substance)"
+          },
+          {
+            "code": "442505006",
+            "display": "Chlamydia trachomatis, serotype Ja (organism)"
+          },
+          {
+            "code": "454431000124102",
+            "display": "Chlamydia trachomatis nucleic acid detected (finding)"
+          },
+          {
+            "code": "59134003",
+            "display": "Lymphogranuloma venereum antigen (substance)"
+          },
+          {
+            "code": "63938009",
+            "display": "Chlamydia trachomatis (organism)"
+          },
+          {
+            "code": "708219005",
+            "display": "Deoxyribonucleic acid of Chlamydia trachomatis L2 (substance)"
+          }
+        ]
+      }
+    ]
+  }
+}

query-connector/src/app/tests/integration/translation.test.ts

@@ -0,0 +1,29 @@
+import { DEFAULT_ERSD_VERSION, ValueSet } from "@/app/constants";
+import ExampleVsacValueSet from "../assets/VSACValueSet.json";
+import { translateVSACToInternalValueSet } from "../../database-service";
+import { ValueSet as FhirValueSet } from "fhir/r4";
+
+const EXPECTED_INTERNAL_VALUESET: ValueSet = {
+  valueSetId: ExampleVsacValueSet.id,
+  valueSetVersion: DEFAULT_ERSD_VERSION,
+  valueSetName: ExampleVsacValueSet.title,
+  author: ExampleVsacValueSet.publisher,
+  system: ExampleVsacValueSet.compose.include[0].system,
+  ersdConceptType: "ostc",
+  dibbsConceptType: "labs",
+  includeValueSet: false,
+  concepts: ExampleVsacValueSet.compose.include[0].concept.map((c) => {
+    return { ...c, include: false };
+  }),
+};
+
+describe("VSAC FHIR response to internal application type", () => {
+  it("translate to expected fixture", async () => {
+    const translationResult = await translateVSACToInternalValueSet(
+      ExampleVsacValueSet as FhirValueSet,
+      "ostc",
+    );
+
+    expect(translationResult).toEqual(EXPECTED_INTERNAL_VALUESET);
+  });
+});