Moved getPMCList to own file

src/index.js

@@ -5,7 +5,8 @@ import "dotenv/config.js";
 import * as fs from "fs";
 import lodash from "lodash";
 import throttledQueue from "throttled-queue";
-import { getPMCList, retrieveFigures } from "./scripts/data-retrieval.js";
+import { retrieveFigures } from "./scripts/data-retrieval.js";
+import { getPMCList } from "./scripts/get-pmc-list.js";
 
 /** Throttled queue for ENTREZ API requests (1 per second) */
 const throttle = throttledQueue(1, 1000);

src/scripts/data-retrieval.js

@@ -8,67 +8,6 @@ const throttle = throttledQueue(1, 1000);
 /** Throttled queue for image downloading (2 per second) */
 const throttleImages = throttledQueue(2, 1000);
 
-/**
- * Retrieve PMCs from NCBI's/NIHs ENTREZ database.
- * @param {String} species Species name(s) to search for (default "Arabidopsis thaliana")
- * @param {Number} maxIDs Maximum number of IDs to return (default 10000000)
- * @returns {Array} List of PMCs
- */
-export async function getPMCList(species = "Arabidopsis thaliana", maxIDs = 10000000) {
-	// Clean arguments
-	species = species.trim().split(" ").join("_");
-	maxIDs = Number.isNaN(maxIDs) ? 10000000 : maxIDs;
-
-	// Build API URL
-	/** ENTREZ's esearch */
-	const base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?";
-	/** Database */
-	const db = "db=pmc&";
-	/** What is being searched for */
-	const term = `term=${species}[Organism]&`;
-	/** Maximum number of publications */
-	const retmax = `retmax=${maxIDs}`;
-
-	/** API's URL */
-	const url = base + db + term + retmax;
-
-	// console feedback
-	console.log(`Retrieving ${species.split("_").join(" ")} PMCs...`);
-
-	// Get and return XML document/data
-	/** API's response */
-	const response = await axios.get(url, {
-		responseType: "document",
-		headers: {
-			"Content-Type": "text/xml",
-		},
-		params: {
-			retmode: "xml",
-		},
-	});
-	/** API's data */
-	const data = response?.data;
-
-	// Go through XML and extract PMCs under eSEarchResult -> IdList -> Id
-	/** PMC list */
-	let pmcList = [];
-
-	if (data) {
-		// Parse the XML string with JSDOM
-		/** JSDOM document */
-		const dom = new JSDOM(data, { contentType: "text/xml" });
-
-		// Use JSDOM to parse XML and get all PMCs
-		pmcList = Array.from(dom.window.document.querySelectorAll("Id")).map((id) => id.textContent);
-
-		console.log(`Found ${pmcList.length} PMCs for ${species.split("_").join(" ")}...`);
-		return pmcList;
-	}
-
-	console.error("No data found...");
-	return pmcList;
-}
-
 /** All data that has already been retrieved */
 let dataRetrieved;
 /** All publications that failed to be scraped or had some issue with them */

src/scripts/get-pmc-list.js

@@ -0,0 +1,63 @@
+import axios from "axios";
+import { JSDOM } from "jsdom";
+
+/**
+ * Retrieve PMCs from NCBI's/NIHs ENTREZ database.
+ * @param {String} species Species name(s) to search for (default "Arabidopsis thaliana")
+ * @param {Number} maxIDs Maximum number of IDs to return (default 10000000)
+ * @returns {Array} List of PMCs
+ */
+export async function getPMCList(species = "Arabidopsis thaliana", maxIDs = 10000000) {
+	// Clean arguments
+	species = species.trim().split(" ").join("_");
+	maxIDs = Number.isNaN(maxIDs) ? 10000000 : maxIDs;
+
+	// Build API URL
+	/** ENTREZ's esearch */
+	const base = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?";
+	/** Database */
+	const db = "db=pmc&";
+	/** What is being searched for */
+	const term = `term=${species}[Organism]&`;
+	/** Maximum number of publications */
+	const retmax = `retmax=${maxIDs}`;
+
+	/** API's URL */
+	const url = base + db + term + retmax;
+
+	// console feedback
+	console.log(`Retrieving ${species.split("_").join(" ")} PMCs...`);
+
+	// Get and return XML document/data
+	/** API's response */
+	const response = await axios.get(url, {
+		responseType: "document",
+		headers: {
+			"Content-Type": "text/xml",
+		},
+		params: {
+			retmode: "xml",
+		},
+	});
+	/** API's data */
+	const data = response?.data;
+
+	// Go through XML and extract PMCs under eSEarchResult -> IdList -> Id
+	/** PMC list */
+	let pmcList = [];
+
+	if (data) {
+		// Parse the XML string with JSDOM
+		/** JSDOM document */
+		const dom = new JSDOM(data, { contentType: "text/xml" });
+
+		// Use JSDOM to parse XML and get all PMCs
+		pmcList = Array.from(dom.window.document.querySelectorAll("Id")).map((id) => id.textContent);
+
+		console.log(`Found ${pmcList.length} PMCs for ${species.split("_").join(" ")}...`);
+		return pmcList;
+	}
+
+	console.error("No data found...");
+	return pmcList;
+}

src/scripts/data-retrieval.test.js → src/scripts/get-pmc-list.test.js

@@ -1,5 +1,5 @@
 import axios from "axios";
-import { getPMCList } from "./data-retrieval";
+import { getPMCList } from "./get-pmc-list";
 
 // Mock the axios module
 jest.mock("axios");