add sample data to nextJS API routes

Author: craigrbarnes

src/lib/AnalysisApps/GWAS/Utils/cohortApi.tsx

@@ -1,7 +1,7 @@
 import { gen3Api, GEN3_API } from '@gen3/core';
 
 const TAGS = 'GWASApp';
-export const GEN3_COHORT_MIDDLEWARE_API = `${GEN3_API}/cohort-middleware`;
+export const GEN3_COHORT_MIDDLEWARE_API =   process.env.NEXT_PUBLIC_GEN3_COHORT_MIDDLEWARE_API || `${GEN3_API}/cohort-middleware`;
 
 const hareConceptId = 2000007027;
 
@@ -11,7 +11,7 @@ export const gwasCohortApiTags = gen3Api.enhanceEndpoints({
 
 // Types for API calls
 
-interface CohortOverlap {
+export interface CohortOverlap {
   cohort_overlap: {
     case_control_overlap: number;
   };
@@ -116,6 +116,18 @@ export interface GWASHistogramResponse {
   bins: Array<GWASHistogramBin>;
 }
 
+/**
+ * Adds a filter to the given covariate array to exclude individuals
+ * who are members of both specified cohorts from analysis. This ensures that
+ * overlapping members in the two cohorts are filtered out based on a
+ * custom dichotomous variable.
+ *
+ * @param {number} cohortId - The identifier for the first cohort.
+ * @param {number} otherCohortId - The identifier for the second cohort.
+ * @param {Array<Covariates>} covariateArray - An array of covariate objects to which
+ *                                             the new filter will be added.
+ * @returns {Array<Covariates>} A new array of covariate objects with the added filter.
+ */
 export const addCDFilter = (
   cohortId: number,
   otherCohortId: number,
@@ -135,6 +147,22 @@ export const addCDFilter = (
   return covariateRequest;
 };
 
+/**
+ * gwasCohortApi is a configuration object used to interact with the GWAS Cohort API.
+ * It provides endpoints to query and transform data related to cohort definitions, sources,
+ * covariates, histogram data, and cohort overlaps. Each endpoint is implemented as a query using
+ * RTK Query `builder.query` and supports fetching and transforming of data for specific use cases.
+ *
+ * Endpoints included:
+ * - getCohortDefinitions: Fetches cohort definitions and statistics by source ID and team project.
+ * - getSources: Retrieves available data sources from the middleware API.
+ * - getSourceId: Extracts the single source ID if only one source is available.
+ * - getCovariates: Fetches covariates based on source ID and predefined concept types.
+ * - getCovariateStats: Retrieves statistics for selected covariates for a given cohort definition.
+ * - getConceptStatsByHareSubset: Fetches concept statistics for a subset of covariates broken down by HARE concept.
+ * - getHistogramInfo: Retrieves histogram data for selected covariates, outcomes, and cohorts.
+ * - getSimpleOverlapInfo: Checks the overlap between two cohorts for selected covariates and outcomes.
+ */
 export const gwasCohortApi = gwasCohortApiTags.injectEndpoints({
   endpoints: (builder) => ({
     getCohortDefinitions: builder.query<

src/lib/AnalysisApps/GWAS/Utils/data/histogram.js

@@ -0,0 +1,34 @@
+import { NextApiRequest, NextApiResponse } from 'next';
+import { CohortOverlap } from '@/lib/AnalysisApps/GWAS/Utils/cohortApi';
+
+interface PathParameters {
+  sourceId: string;
+  cohortAId: string;
+  cohortBId: string;
+}
+const handler = async (req: NextApiRequest, res: NextApiResponse) => {
+  // Get the sourceId from the slug in the path
+  const { query } = req;
+  // eslint-disable-next-line @typescript-eslint/no-unused-vars
+  const { sourceId, cohortAId, cohortBId } = query as unknown as PathParameters; // messy but this is for development
+
+  const data: Record<string, Record<string, CohortOverlap>> = {
+    '1537': {
+      '446': { cohort_overlap: { case_control_overlap: 236021 } },
+      '2356': { cohort_overlap: { case_control_overlap: 236021 } },
+    },
+    '446': {
+      '2356': { cohort_overlap: { case_control_overlap: 648242 } },
+    },
+  };
+
+  if (data[cohortAId] && data[cohortAId][cohortBId]) {
+    return res.status(200).json(data[cohortAId][cohortBId]);
+  }
+  if (data[cohortBId] && data[cohortBId][cohortAId]) {
+    return res.status(200).json(data[cohortBId][cohortAId]);
+  }
+  return res.status(200).json({ cohort_overlap: { case_control_overlap: 648242 }});
+
+};
+export default handler;

src/pages/api/cohort-stats/check-overlap/by-source-id/[sourceId]/by-cohort-definition-ids/[cohortAId]/[cohortBId]/index.ts

@@ -0,0 +1,33 @@
+import { NextApiRequest, NextApiResponse } from 'next';
+
+const handler = async (req: NextApiRequest, res: NextApiResponse) => {
+
+  // Get the sourceId from the slug in the path
+  // const { query } = req;
+  // const { sourceId } = query;
+  return res.status(200).json({
+    cohort_definitions_and_stats: [
+      {
+        cohort_definition_id: 573,
+        cohort_name: 'team2 - test new cohort - catch all',
+        size: 70240,
+      },
+      {
+        cohort_definition_id: 559,
+        cohort_name: 'test new cohort - catch all',
+        size: 70240,
+      },
+      {
+        cohort_definition_id: 574,
+        cohort_name: 'team2 - test new cohort - medium + large',
+        size: 23800,
+      },
+      {
+        cohort_definition_id: 575,
+        cohort_name: 'team2 - test new cohort - small',
+        size: 80,
+      },
+    ],
+  });
+};
+export default handler;