Merge branch 'main' into kcd/16-rework-name-regex-on-patient-search-page

query-connector/e2e/alternate_queries.spec.ts

@@ -42,9 +42,8 @@ test.describe("alternate queries with the Query Connector", () => {
     await expect(page.getByText(TEST_PATIENT.MRN)).toBeVisible();
   });
 
-  test("social determinants query with generalized function", async ({
-    page,
-  }) => {
+  // test("social determinants query with generalized function", async ({
+  test("cancer query with generalized function", async ({ page }) => {
     await page.getByRole("button", { name: "Go to the demo" }).click();
     await page.getByRole("button", { name: "Fill fields" }).click();
     await page.getByRole("button", { name: "Search for patient" }).click();
@@ -54,7 +53,8 @@ test.describe("alternate queries with the Query Connector", () => {
     await expect(
       page.getByRole("heading", { name: "Select a query" }),
     ).toBeVisible();
-    await page.getByTestId("Select").selectOption("social-determinants");
+    // await page.getByTestId("Select").selectOption("social-determinants");
+    await page.getByTestId("Select").selectOption("cancer");
     await page.getByRole("button", { name: "Submit" }).click();
     await expect(page.getByText("Loading")).toHaveCount(0, { timeout: 10000 });
 

query-connector/src/app/constants.ts

@@ -40,10 +40,11 @@ export const demoQueryOptions = [
   { value: "chlamydia", label: "Chlamydia case investigation" },
   { value: "gonorrhea", label: "Gonorrhea case investigation" },
   { value: "newborn-screening", label: "Newborn screening follow-up" },
-  {
-    value: "social-determinants",
-    label: "Gather social determinants of health",
-  },
+  // Temporarily remove social determinants
+  // {
+  //   value: "social-determinants",
+  //   label: "Gather social determinants of health",
+  // },
   { value: "syphilis", label: "Syphilis case investigation" },
 ];
 
@@ -386,3 +387,18 @@ export function isFhirResource(resource: unknown): resource is FhirResource {
     "resourceType" in resource
   );
 }
+
+// The value for "concept version" (sometimes) exists under "expansion" in the VSAC FHIR
+// response. This is similar, but different in some subtle ways from the "compose.include"
+// path that we're currently using to grab concept information. Although we could
+// grab and parse this information from the FHIR response, it would involve
+// changing our data model to store information that we think is a "nice to
+// have", which is only available sometimes. As a result, we're purposefully
+// leaving this blank until we can clean up the migration schema to drop these columns
+export const INTENTIONAL_EMPTY_STRING_FOR_CONCEPT_VERSION = "";
+
+// Originally, the column in the concept table was set up to maintain backwards e
+//compatibility with the ICD-9 codes that the team is deciding not to support after
+// we clean up the DB migration. Leaving these in until we can clean these up
+// in the migration schema
+export const INTENTIONAL_EMPTY_STRING_FOR_GEM_CODE = "";

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

@@ -3,8 +3,9 @@ import { Pool, PoolConfig, QueryResultRow } from "pg";
 import { Bundle, OperationOutcome, ValueSet as FhirValueSet } from "fhir/r4";
 import {
   Concept,
-  DEFAULT_ERSD_VERSION,
   ErsdConceptType,
+  INTENTIONAL_EMPTY_STRING_FOR_CONCEPT_VERSION,
+  INTENTIONAL_EMPTY_STRING_FOR_GEM_CODE,
   ValueSet,
   ersdToDibbsConceptMap,
 } from "./constants";
@@ -184,7 +185,7 @@ export async function translateVSACToInternalValueSet(
   ersdConceptType: ErsdConceptType,
 ) {
   const id = fhirValueset.id;
-  const version = DEFAULT_ERSD_VERSION;
+  const version = fhirValueset.version;
 
   const name = fhirValueset.title;
   const author = fhirValueset.publisher;
@@ -207,3 +208,141 @@ export async function translateVSACToInternalValueSet(
     concepts: concepts,
   } as ValueSet;
 }
+
+/**
+ * Function call to insert a new ValueSet into the database.
+ * @param vs - a ValueSet in of the shape of our internal data model to insert
+ * @returns success / failure information, as well as errors as appropriate
+ */
+export async function insertValueSet(vs: ValueSet) {
+  let errorArray: string[] = [];
+
+  const insertValueSetPromise = generateValueSetSqlPromise(vs);
+  try {
+    await insertValueSetPromise;
+  } catch (e) {
+    console.error(
+      `ValueSet insertion for ${vs.valueSetId}_${vs.valueSetVersion} failed`,
+    );
+    console.error(e);
+    errorArray.push("Error occured in valuset insertion");
+  }
+
+  const insertConceptsPromiseArray = generateConceptSqlPromises(vs);
+  const conceptInsertResults = await Promise.allSettled(
+    insertConceptsPromiseArray,
+  );
+
+  const allConceptInsertsSucceed = conceptInsertResults.every(
+    (r) => r.status === "fulfilled",
+  );
+
+  if (!allConceptInsertsSucceed) {
+    logRejectedPromiseReasons(conceptInsertResults, "Concept insertion failed");
+    errorArray.push("Error occured in concept insertion");
+  }
+
+  const joinInsertsPromiseArray = generateValuesetConceptJoinSqlPromises(vs);
+  const joinInsertResults = await Promise.allSettled(joinInsertsPromiseArray);
+
+  const allJoinInsertsSucceed = joinInsertResults.every(
+    (r) => r.status === "fulfilled",
+  );
+
+  if (!allJoinInsertsSucceed) {
+    logRejectedPromiseReasons(
+      joinInsertResults,
+      "ValueSet <> concept join insert failed",
+    );
+    errorArray.push("Error occured in ValueSet <> concept join seeding");
+  }
+
+  if (errorArray.length === 0) return { success: true };
+  return { success: false, error: errorArray.join(",") };
+}
+
+/**
+ * Helper function to generate the SQL needed for valueset insertion.
+ * @param vs - The ValueSet in of the shape of our internal data model to insert
+ * @returns The SQL statement for insertion
+ */
+function generateValueSetSqlPromise(vs: ValueSet) {
+  const valueSetOid = vs.valueSetId;
+
+  const valueSetUniqueId = `${valueSetOid}_${vs.valueSetVersion}`;
+  const insertValueSetSql =
+    "INSERT INTO valuesets VALUES($1,$2,$3,$4,$5,$6) RETURNING id;";
+  const valuesArray = [
+    valueSetUniqueId,
+    valueSetOid,
+    vs.valueSetVersion,
+    vs.valueSetName,
+    vs.author,
+    vs.ersdConceptType,
+  ];
+
+  return dbClient.query(insertValueSetSql, valuesArray);
+}
+
+/**
+ * Helper function to generate the SQL needed for concept / valueset join insertion
+ * needed during valueset creation.
+ * @param vs - The ValueSet in of the shape of our internal data model to insert
+ * @returns The SQL statement array for all concepts for insertion
+ */
+function generateConceptSqlPromises(vs: ValueSet) {
+  const insertConceptsSqlArray = vs.concepts.map((concept) => {
+    const systemPrefix = stripProtocolAndTLDFromSystemUrl(vs.system);
+    const conceptUniqueId = `${systemPrefix}_${concept.code}`;
+    const insertConceptSql = `INSERT INTO concepts VALUES($1,$2,$3,$4,$5,$6) RETURNING id;`;
+    const conceptInsertPromise = dbClient.query(insertConceptSql, [
+      conceptUniqueId,
+      concept.code,
+      vs.system,
+      concept.display,
+      // see notes in constants file for the intentional empty strings
+      INTENTIONAL_EMPTY_STRING_FOR_GEM_CODE,
+      INTENTIONAL_EMPTY_STRING_FOR_CONCEPT_VERSION,
+    ]);
+
+    return conceptInsertPromise;
+  });
+
+  return insertConceptsSqlArray;
+}
+
+function generateValuesetConceptJoinSqlPromises(vs: ValueSet) {
+  const valueSetUniqueId = `${vs.valueSetId}_${vs.valueSetVersion}`;
+  const insertConceptsSqlArray = vs.concepts.map((concept) => {
+    const systemPrefix = stripProtocolAndTLDFromSystemUrl(vs.system);
+    const conceptUniqueId = `${systemPrefix}_${concept.code}`;
+    const insertJoinSql = `INSERT INTO valueset_to_concept VALUES($1,$2, $3) RETURNING valueset_id, concept_id;`;
+    const conceptInsertPromise = dbClient.query(insertJoinSql, [
+      `${valueSetUniqueId}_${conceptUniqueId}`,
+      valueSetUniqueId,
+      conceptUniqueId,
+    ]);
+
+    return conceptInsertPromise;
+  });
+
+  return insertConceptsSqlArray;
+}
+
+function stripProtocolAndTLDFromSystemUrl(systemURL: string) {
+  const match = systemURL.match(/https?:\/\/([^\.]+)/);
+  return match ? match[1] : systemURL;
+}
+
+function logRejectedPromiseReasons<T>(
+  resultsArray: PromiseSettledResult<T>[],
+  errorMessageString: string,
+) {
+  return resultsArray
+    .filter((r): r is PromiseRejectedResult => r.status === "rejected")
+    .map((r) => {
+      console.error(errorMessageString);
+      console.error(r.reason);
+      return r.reason;
+    });
+}

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

@@ -1,11 +1,11 @@
-import { DEFAULT_ERSD_VERSION, ValueSet } from "@/app/constants";
+import { 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,
+  valueSetVersion: ExampleVsacValueSet.version,
   valueSetName: ExampleVsacValueSet.title,
   author: ExampleVsacValueSet.publisher,
   system: ExampleVsacValueSet.compose.include[0].system,