Merge branch 'main' into nickclyde/keycloak-terraform

CDCgov · Jan 30, 2025 · 6df0f46 · 6df0f46
2 parents 8a034fc + d71aa45
commit 6df0f46
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diff --git a/query-connector/flyway/sql/V06_01__add_immunization_flag_to_query_table.sql b/query-connector/flyway/sql/V06_01__add_immunization_flag_to_query_table.sql
@@ -0,0 +1,2 @@
+ALTER TABLE query 
+ADD COLUMN immunization BOOLEAN DEFAULT FALSE;
diff --git a/query-connector/integration.sh b/query-connector/integration.sh
@@ -5,7 +5,7 @@ set -e  # Exit immediately if a command exits with a non-zero status
 docker compose -f docker-compose-integration.yaml up -d
 
 # wait for flyway to finish running before...
-docker compose -f docker-compose-integration.yaml logs -f flyway | grep -q "Successfully applied"
+docker compose -f docker-compose-integration.yaml logs -f flyway | grep -q "Successfully applied\|No migration necessary"
 
 # running our integration tests
 DATABASE_URL=postgresql://postgres:pw@localhost:5432/tefca_db TEST_TYPE=integration jest --testPathPattern=tests/integration

diff --git a/query-connector/jest.config.js b/query-connector/jest.config.js
@@ -13,6 +13,7 @@ const createJestConfig = nextJest({
 const customJestConfig = {
   setupFilesAfterEnv: ["<rootDir>/jest.setup.ts"],
   testEnvironment: "jest-fixed-jsdom",
+  modulePathIgnorePatterns: ["<rootDir>/.next/"],
 };
 
 // createJestConfig is exported this way to ensure that next/jest can load the Next.js config which is async

diff --git a/query-connector/src/app/(pages)/query/components/selectQuery/queryHooks.ts b/query-connector/src/app/(pages)/query/components/selectQuery/queryHooks.ts
@@ -13,8 +13,14 @@ type SetStateCallback<T> = React.Dispatch<React.SetStateAction<T>>;
  */
 export async function fetchQueryValueSets(queryName: string) {
   const queryResults = await getSavedQueryByName(queryName);
-  const valueSets = unnestValueSetsFromQuery(queryResults);
+  if (queryResults === undefined) {
+    console.error(
+      `Query by name ${queryName} not found. Returning no value sets`,
+    );
+    return [];
+  }
 
+  const valueSets = unnestValueSetsFromQuery(queryResults);
   return valueSets;
 }
 

diff --git a/query-connector/src/app/(pages)/queryBuilding/buildFromTemplates/BuildFromTemplates.test.tsx b/query-connector/src/app/(pages)/queryBuilding/buildFromTemplates/BuildFromTemplates.test.tsx
@@ -1,22 +1,22 @@
-import { screen, waitFor } from "@testing-library/react";
+import BuildFromTemplates from "@/app/(pages)/queryBuilding/buildFromTemplates/BuildFromTemplates";
+import {
+  DEFAULT_QUERIES,
+  conditionIdToNameMap,
+  categoryToConditionNameArrayMap,
+  gonorreheaValueSets,
+  gonorreheaSavedQuery,
+  cancerValueSets,
+} from "@/app/(pages)/queryBuilding/fixtures";
+import { formatDiseaseDisplay } from "@/app/(pages)/queryBuilding/utils";
+import { getSavedQueryById } from "@/app/backend/query-building";
 import { DataContext } from "@/app/shared/DataProvider";
+import { USE_CASE_DETAILS } from "@/app/shared/constants";
 import {
   getConditionsData,
   getValueSetsAndConceptsByConditionIDs,
-} from "../../../shared/database-service";
-import {
-  cancerValueSets,
-  categoryToConditionNameArrayMap,
-  conditionIdToNameMap,
-  DEFAULT_QUERIES,
-  gonorreheaSavedQuery,
-  gonorreheaValueSets,
-} from "../fixtures";
-import BuildFromTemplates from "./BuildFromTemplates";
-import { formatDiseaseDisplay } from "../utils";
+} from "@/app/shared/database-service";
 import { renderWithUser } from "@/app/tests/unit/setup";
-import { USE_CASE_DETAILS } from "@/app/shared/constants";
-import { getSavedQueryById } from "@/app/backend/query-building";
+import { screen, waitFor } from "@testing-library/dom";
 import { CONDITION_DRAWER_SEARCH_PLACEHOLDER } from "../components/constants";
 
 jest.mock("../../../shared/database-service", () => ({
@@ -255,7 +255,7 @@ describe("tests the valueset selection page interactions", () => {
 
   it("filters search on the valueset selection drawer appropriately", async () => {
     const GONORREHEA_VALUESET_MAP = Object.values(
-      gonorreheaSavedQuery[0].query_data,
+      gonorreheaSavedQuery.query_data,
     )[0];
     const GONORREHEA_VALUESET_IDS = Object.keys(GONORREHEA_VALUESET_MAP);
 

diff --git a/query-connector/src/app/(pages)/queryBuilding/buildFromTemplates/BuildFromTemplates.tsx b/query-connector/src/app/(pages)/queryBuilding/buildFromTemplates/BuildFromTemplates.tsx
@@ -122,12 +122,11 @@ const BuildFromTemplates: React.FC<BuildFromTemplatesProps> = ({
       if (selectedQuery.queryId === undefined) {
         return;
       }
-      const result = await getSavedQueryById(selectedQuery.queryId);
-      if (result === undefined) {
-        return; // todo: error???
+      const savedQuery = await getSavedQueryById(selectedQuery.queryId);
+      if (savedQuery === undefined) {
+        return;
       }
       const initialState: NestedQuery = {};
-      const savedQuery = result[0];
 
       Object.entries(savedQuery.query_data).forEach(
         ([conditionId, valueSetMap]) => {

diff --git a/query-connector/src/app/(pages)/queryBuilding/components/ConceptSelection.tsx b/query-connector/src/app/(pages)/queryBuilding/components/ConceptSelection.tsx
@@ -1,8 +1,8 @@
 import React from "react";
 import styles from "../buildFromTemplates/conditionTemplateSelection.module.scss";
+import { ConceptDisplay } from "./SelectionViewAccordionBody";
 import { showToastConfirmation } from "@/app/ui/designSystem/toast/Toast";
 import Checkbox from "@/app/ui/designSystem/checkbox/Checkbox";
-import { ConceptDisplay } from "./SelectionViewAccordionBody";
 
 type ConceptSelectionProps = {
   concepts: ConceptDisplay[];

diff --git a/query-connector/src/app/(pages)/queryBuilding/fixtures.ts b/query-connector/src/app/(pages)/queryBuilding/fixtures.ts
@@ -1,4 +1,4 @@
-import { QueryDetailsResult } from "./utils";
+import { QueryTableResult } from "./utils";
 
 // Fixture shortened significantly for maintenance purposes
 export const DEFAULT_QUERIES = [
@@ -605,132 +605,126 @@ export const cancerValueSets = [
   },
 ];
 
-export const gonorreheaSavedQuery: QueryDetailsResult[] = [
-  {
-    query_id: "73e1a777-49cb-4e19-bc71-8c3fd3ffda64",
-    query_name: "Gonorrhea case investigation",
-    conditions_list: ["15628003"],
-    query_data: {
-      "15628003": {
-        "2.16.840.1.113762.1.4.1146.1036_20190605": {
-          valueSetId: "2.16.840.1.113762.1.4.1146.1036_20190605",
-          valueSetVersion: "20190605",
-          valueSetName:
-            "Gonorrhea [Neisseria species Unspecified] (Organism or Substance in Lab Results)",
-          valueSetExternalId: "2.16.840.1.113762.1.4.1146.1036",
-          author: "CSTE Steward",
-          system: "http://snomed.info/sct",
-          ersdConceptType: "labs",
-          dibbsConceptType: "labs",
-          includeValueSet: true,
-          concepts: [
-            {
-              code: "715869002",
-              display:
-                "Neisseria species, not Neisseria meningitidis (organism)",
-              include: true,
-            },
-            {
-              code: "414811005",
-              display: "Neisseria species not Neisseria gonococci (organism)",
-              include: true,
-            },
-            {
-              code: "59083001",
-              display: "Genus Neisseria (organism)",
-              include: true,
-            },
-            {
-              code: "715872009",
-              display:
-                "Neisseria species, not Neisseria gonorrhoeae and not Neisseria meningitidis (organism)",
-              include: true,
-            },
-          ],
-        },
-        "2.16.840.1.113762.1.4.1146.169_20230602": {
-          valueSetId: "2.16.840.1.113762.1.4.1146.169_20230602",
-          valueSetVersion: "20230602",
-          valueSetName:
-            "Gonorrhea [Neisseria gonorrhoeae] (Organism or Substance in Lab Results)",
-          valueSetExternalId: "2.16.840.1.113762.1.4.1146.169",
-          author: "CSTE Steward",
-          system: "http://snomed.info/sct",
-          ersdConceptType: "labs",
-          dibbsConceptType: "labs",
-          includeValueSet: true,
-          concepts: [
-            {
-              code: "277504006",
-              display:
-                "Spectinomycin-resistant Neisseria gonorrhoeae (organism)",
-              include: true,
-            },
-            {
-              code: "120977006",
-              display: "Antigen of Neisseria gonorrhoeae (substance)",
-              include: true,
-            },
-            {
-              code: "703483000",
-              display:
-                "Deoxyribonucleic acid of Neisseria gonorrhoeae (substance)",
-              include: true,
-            },
-            {
-              code: "277501003",
-              display:
-                "Penicillinase-producing Neisseria gonorrhoeae (organism)",
-              include: true,
-            },
-            {
-              code: "409805000",
-              display:
-                "Fluoroquinolone-resistant Neisseria gonorrhoeae (organism)",
-              include: true,
-            },
-            {
-              code: "277502005",
-              display:
-                "Tetracycline-resistant Neisseria gonorrhoeae (organism)",
-              include: true,
-            },
-            {
-              code: "469831000124106",
-              display: "Neisseria gonorrhoeae subspecies kochii (organism)",
-              include: true,
-            },
-            {
-              code: "454421000124100",
-              display: "Neisseria gonorrhoeae nucleic acid detected (finding)",
-              include: true,
-            },
-            {
-              code: "121172006",
-              display:
-                "Ribosomal ribonucleic acid of Neisseria gonorrhoeae (substance)",
-              include: true,
-            },
-            {
-              code: "68704007",
-              display: "Neisseria gonorrhoeae (organism)",
-              include: true,
-            },
-            {
-              code: "277503000",
-              display:
-                "Cephalosporin-resistant Neisseria gonorrhoeae (organism)",
-              include: true,
-            },
-            {
-              code: "414809001",
-              display:
-                "Neisseria gonorrhoeae, beta lactamase negative (organism)",
-              include: true,
-            },
-          ],
-        },
+export const gonorreheaSavedQuery: QueryTableResult = {
+  query_id: "73e1a777-49cb-4e19-bc71-8c3fd3ffda64",
+  query_name: "Gonorrhea case investigation",
+  conditions_list: ["15628003"],
+  query_data: {
+    "15628003": {
+      "2.16.840.1.113762.1.4.1146.1036_20190605": {
+        valueSetId: "2.16.840.1.113762.1.4.1146.1036_20190605",
+        valueSetVersion: "20190605",
+        valueSetName:
+          "Gonorrhea [Neisseria species Unspecified] (Organism or Substance in Lab Results)",
+        valueSetExternalId: "2.16.840.1.113762.1.4.1146.1036",
+        author: "CSTE Steward",
+        system: "http://snomed.info/sct",
+        ersdConceptType: "labs",
+        dibbsConceptType: "labs",
+        includeValueSet: true,
+        concepts: [
+          {
+            code: "715869002",
+            display: "Neisseria species, not Neisseria meningitidis (organism)",
+            include: true,
+          },
+          {
+            code: "414811005",
+            display: "Neisseria species not Neisseria gonococci (organism)",
+            include: true,
+          },
+          {
+            code: "59083001",
+            display: "Genus Neisseria (organism)",
+            include: true,
+          },
+          {
+            code: "715872009",
+            display:
+              "Neisseria species, not Neisseria gonorrhoeae and not Neisseria meningitidis (organism)",
+            include: true,
+          },
+        ],
+      },
+      "2.16.840.1.113762.1.4.1146.169_20230602": {
+        valueSetId: "2.16.840.1.113762.1.4.1146.169_20230602",
+        valueSetVersion: "20230602",
+        valueSetName:
+          "Gonorrhea [Neisseria gonorrhoeae] (Organism or Substance in Lab Results)",
+        valueSetExternalId: "2.16.840.1.113762.1.4.1146.169",
+        author: "CSTE Steward",
+        system: "http://snomed.info/sct",
+        ersdConceptType: "labs",
+        dibbsConceptType: "labs",
+        includeValueSet: true,
+        concepts: [
+          {
+            code: "277504006",
+            display: "Spectinomycin-resistant Neisseria gonorrhoeae (organism)",
+            include: true,
+          },
+          {
+            code: "120977006",
+            display: "Antigen of Neisseria gonorrhoeae (substance)",
+            include: true,
+          },
+          {
+            code: "703483000",
+            display:
+              "Deoxyribonucleic acid of Neisseria gonorrhoeae (substance)",
+            include: true,
+          },
+          {
+            code: "277501003",
+            display: "Penicillinase-producing Neisseria gonorrhoeae (organism)",
+            include: true,
+          },
+          {
+            code: "409805000",
+            display:
+              "Fluoroquinolone-resistant Neisseria gonorrhoeae (organism)",
+            include: true,
+          },
+          {
+            code: "277502005",
+            display: "Tetracycline-resistant Neisseria gonorrhoeae (organism)",
+            include: true,
+          },
+          {
+            code: "469831000124106",
+            display: "Neisseria gonorrhoeae subspecies kochii (organism)",
+            include: true,
+          },
+          {
+            code: "454421000124100",
+            display: "Neisseria gonorrhoeae nucleic acid detected (finding)",
+            include: true,
+          },
+          {
+            code: "121172006",
+            display:
+              "Ribosomal ribonucleic acid of Neisseria gonorrhoeae (substance)",
+            include: true,
+          },
+          {
+            code: "68704007",
+            display: "Neisseria gonorrhoeae (organism)",
+            include: true,
+          },
+          {
+            code: "277503000",
+            display: "Cephalosporin-resistant Neisseria gonorrhoeae (organism)",
+            include: true,
+          },
+          {
+            code: "414809001",
+            display:
+              "Neisseria gonorrhoeae, beta lactamase negative (organism)",
+            include: true,
+          },
+        ],
       },
     },
   },
-];
+  immunization: false,
+};
diff --git a/query-connector/src/app/(pages)/queryBuilding/utils.ts b/query-connector/src/app/(pages)/queryBuilding/utils.ts
@@ -32,11 +32,12 @@ export type QueryUpdateResult = {
 export type QueryDataColumn = {
   [conditionId: string]: { [valueSetId: string]: DibbsValueSet };
 };
-export type QueryDetailsResult = {
+export type QueryTableResult = {
   query_name: string;
   query_id: string;
   query_data: QueryDataColumn;
   conditions_list: string[];
+  immunization: boolean;
 };
 
 export const EMPTY_QUERY_SELECTION = {

diff --git a/query-connector/src/app/api/query/route.ts b/query-connector/src/app/api/query/route.ts
@@ -90,14 +90,14 @@ export async function POST(request: NextRequest) {
 
   const queryResults = await getSavedQueryById(id);
 
-  if (queryResults.length === 0) {
+  if (queryResults === undefined) {
     const OperationOutcome = await handleRequestError(INVALID_QUERY);
     return NextResponse.json(OperationOutcome);
   }
 
   // Add params & patient identifiers to QueryName
   const QueryRequest: QueryRequest = {
-    query_name: queryResults[0].query_name,
+    query_name: queryResults.query_name,
     fhir_server: fhir_server,
     ...(PatientIdentifiers.first_name && {
       first_name: PatientIdentifiers.first_name,
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		ALTER TABLE query
		ADD COLUMN immunization BOOLEAN DEFAULT FALSE;