Fix XML generator not generating XMLs

Makefile

@@ -8,7 +8,7 @@ validate-all: py-validate
 	Rscript -e 'renv::restore()'
 
 # === Python Commands for eFP-Seq_Browser ===
-.PHONY: py-install py-format py-lint py-test py-clean py-validate
+.PHONY: py-install py-format py-lint py-validate
 
 PY_FILES = cgi-bin/*.cgi
 
@@ -21,4 +21,4 @@ py-format:
 py-lint:
 	uv run ruff check --fix $(PY_FILES)
 
-py-validate: py-install py-format py-lint
+py-validate: py-format py-lint

cgi-bin/Submission_page/XMLgenerator.js

@@ -329,44 +329,26 @@ function check_links(bam_name, repo_name) {
 	for (let i = 0; i < x.length; i++) {
 		if (x[i].id === "bam_input") {
 			if (x[i].value.length > 0) {
-				if (bam_x[i].value == "Google Drive") {
-					// Verify if Google Link
-					const driveLink = x[i].value.split("//");
-					if (driveLink.length > 1) {
-						// If starts with https
-						const driveURL = driveLink[1];
-						return (
-							driveURL.split("/")[0] === "drive.google.com" ||
-							driveURL.split("/")[0] === "www.drive.google.com"
-						);
-					} else if (driveLink.length === 0) {
-						// If does not start with https
-						return (
-							driveLink.split("/")[0] === "drive.google.com" ||
-							driveLink.split("/")[0] === "www.drive.google.com"
-						);
-					} else {
-						// Not URL
-						return false;
-					}
-				} else if (bam_x[i].value == "Amazon AWS") {
-					/** Link from string to URL format */
-					const urlString = new URL(x[i].value);
+				let urlString;
+				try {
+					urlString = new URL(x[i].value);
+				} catch {
+					return false;
+				}
+
+				const hostValue = urlString?.host ?? "";
 
+				if (bam_x[i].value === "Google Drive") {
+					return ["drive.google.com", "www.drive.google.com"].includes(hostValue);
+				} else if (bam_x[i].value === "Amazon AWS") {
 					if (
-						(urlString.host("s3.amazonaws.com") || x[i].value.includes("araport.cyverse-cdn.tacc.cloud")) &&
-						check_amazon_for_bam(x[i].value)
+						check_amazon_for_bam(x[i].value) &&
+						(["s3.amazonaws.com", "araport.cyverse-cdn.tacc.cloud"].includes(hostValue) ||
+							x[i].value.includes("araport.cyverse-cdn.tacc.cloud"))
 					) {
 						return true;
-					} else if (
-						(urlString.host("s3.amazonaws.com") ||
-							x[i].value.includes("araport.cyverse-cdn.tacc.cloud/")) &&
-						check_amazon_for_bam(x[i].value)
-					) {
-						return false;
-					} else {
-						return false;
 					}
+					return false;
 				} else {
 					return false;
 				}
@@ -507,19 +489,21 @@ function outline_links(bam_name, repo_name) {
 
 				/** URL for the hosted BAM file */
 				let urlValue;
+				let hostValue = "";
 
-				// Convert the
+				// Convert the string into a URL object if valid
 				try {
 					urlValue = new URL(x[i].value);
+					hostValue = urlValue.host || "";
 				} catch {
 					console.error("Unreadable URL presented: ", x[i].value);
 				}
 
-				if (bamHostType && urlValue) {
+				if (bamHostType && hostValue) {
 					if (bamHostType === "Amazon AWS") {
 						if (
 							check_amazon_for_bam(x[i].value) &&
-							["s3.amazonaws.com", "araport.cyverse-cdn.tacc.cloud"].includes(urlValue[host])
+							["s3.amazonaws.com", "araport.cyverse-cdn.tacc.cloud"].includes(hostValue)
 						) {
 							x[i].style.borderColor = null;
 							x[i].style.boxShadow = null;
@@ -528,7 +512,7 @@ function outline_links(bam_name, repo_name) {
 							x[i].style.boxShadow = "0 0 10px #ff2626";
 						}
 					} else if (bamHostType === "Google Drive") {
-						if (["drive.google.com"].includes(urlValue[host])) {
+						if (["drive.google.com", "www.drive.google.com"].includes(hostValue)) {
 							x[i].style.borderColor = null;
 							x[i].style.boxShadow = null;
 						} else {
@@ -1300,3 +1284,12 @@ function initGen() {
 setTimeout(function () {
 	initGen();
 }, 1000);
+
+// Export functions for testing in Node.js environments
+if (typeof module !== "undefined" && module.exports) {
+	module.exports = {
+		update,
+		check_links,
+		check_amazon_for_bam,
+	};
+}

cgi-bin/Submission_page/XMLgenerator.test.js

@@ -2,59 +2,53 @@
  * @jest-environment jsdom
  */
 
-const fs = require("fs");
-const path = require("path");
+const elementValueMap = {
+	reqxml: { value: "TestXML" },
+	reqauthor: { value: "Author" },
+	contectinfo: { value: "contact@email.com" },
+};
 
-describe("update (XMLgenerator.js)", () => {
-	let update;
-	let $;
+// Lightweight jQuery stub to satisfy update()
+global.$ = function () {
+	const valueMap = {
+		".channelcontrols": "ctrl1, ctrl2",
+		".channelgroupwidtho": "rep1, rep2",
+		".channeldescription": "desc",
+		".channelrecordnumber": "42",
+		".channelhexcolor": "#ff0000",
+		".channelbamType": "Google Drive",
+		".channelbamlink": "https://drive.google.com/file/d/abc",
+		".channeltotalreadsmapped": "12345",
+		".channelreadmapmethod": "STAR",
+		".channelpublicationlink": "https://pub.com/xyz",
+		".channeltissue": "Leaf",
+		".channelsvgname": "ath-leaf.svg",
+		".channeltitle": "Test Title",
+		".channelsralink": "SRR000001",
+		".channelspecies": "Arabidopsis",
+		".channelforeground": "#000000",
+		".channelfilename": "file1.bam",
+	};
 
-	beforeAll(() => {
-		// Minimal jQuery mock
-		$ = () => ({
-			find: (selector) => ({
-				val: () => {
-					const map = {
-						".channelcontrols": "ctrl1, ctrl2",
-						".channelgroupwidtho": "rep1, rep2",
-						".channeldescription": "desc",
-						".channelrecordnumber": "42",
-						".channelhexcolor": "#ff0000",
-						".channelbamType": "Google Drive",
-						".channelbamlink": "https://drive.google.com/file/d/abc",
-						".channeltotalreadsmapped": "12345",
-						".channelreadmapmethod": "STAR",
-						".channelpublicationlink": "https://pub.com/xyz",
-						".channeltissue": "Leaf",
-						".channelsvgname": "ath-leaf.svg",
-						".channeltitle": "Test Title",
-						".channelsralink": "SRR000001",
-						".channelspecies": "Arabidopsis",
-						".channelforeground": "#000000",
-						".channelfilename": "file1.bam",
-					};
-					return map[selector] || "dummy";
-				},
-			}),
-		});
+	return {
+		find: (childSelector) => ({ val: () => valueMap[childSelector] || "" }),
+	};
+};
+global.$.fn = {};
 
-		// Robust document.getElementById mock for all ids
-		const getElementByIdMock = (id) => {
-			const values = {
-				reqxml: { value: "TestXML" },
-				reqauthor: { value: "Author" },
-				contectinfo: { value: "contact@email.com" },
-			};
-			return values[id] || { value: "dummy" };
-		};
-		if (global.document) {
-			global.document.getElementById = getElementByIdMock;
-		} else {
-			global.document = { getElementById: getElementByIdMock };
-		}
-		global.$ = $;
+// Mock document.getElementById before requiring modules
+global.document = {
+	...global.document,
+	getElementById: (id) => elementValueMap[id] || { value: "" },
+};
+
+const xmlGeneratorModule = require("./XMLgenerator.js");
 
-		// Required top-level variables for update()
+describe("XMLgenerator", () => {
+	const { update, check_links, check_amazon_for_bam } = xmlGeneratorModule;
+
+	beforeEach(() => {
+		global.document.getElementById = (id) => elementValueMap[id] || { value: "" };
 		global.topXML = [
 			'\t\t<file info="<?channeldescription?>" record_number="<?channelrecordnumber?>" foreground="<?channelforeground?>" hex_colour="<?channelhexcolor?>" bam_type="<?channelbamType?>" name="<?channelbamlink?>" filename="<?channelfilename?>" total_reads_mapped="<?channeltotalreadsmapped?>" read_map_method="<?channelreadmapmethod?>" publication_link="<?channelpublicationlink?>" svg_subunit="<?channeltissue?>" svgname="<?channelsvgname?>" description="<?channeltitle?>" url="<?channelsralink?>" species="<?channelspecies?>" title="<?channeligbtitle?>">',
 			"\t\t\t<controls>\n",
@@ -65,30 +59,109 @@ describe("update (XMLgenerator.js)", () => {
 		global.existingXML = "";
 		global.all_controls = "";
 		global.all_replicates = "";
+	});
+
+	describe("update", () => {
+		const cases = [
+			{
+				name: "includes all substituted values",
+				want: [
+					"desc",
+					'record_number="42"',
+					'hex_colour="#ff0000"',
+					'bam_type="Google Drive"',
+					'name="https://drive.google.com/file/d/abc"',
+					'filename="file1.bam"',
+					"<bam_exp>ctrl1</bam_exp>",
+					"<bam_exp>rep2</bam_exp>",
+					'total_reads_mapped="12345"',
+					'read_map_method="STAR"',
+					'species="Arabidopsis"',
+					'svg_subunit="Leaf"',
+				],
+			},
+		];
+
+		it.each(cases)("$name", ({ want }) => {
+			const result = update("", {});
+			want.forEach((expected) => expect(result).toContain(expected));
+			expect(result).toContain("</file>");
+		});
+	});
 
-		// Load the update function from XMLgenerator.js
-		const code = fs.readFileSync(path.join(__dirname, "../Submission_page/XMLgenerator.js"), "utf8");
-		const fnMatch = code.match(/function update\s*\(([^)]*)\)\s*{([\s\S]*?)^}/m);
-		if (!fnMatch) throw new Error("update function not found in XMLgenerator.js");
-		const args = fnMatch[1];
-		const body = fnMatch[2];
+	describe("check_amazon_for_bam", () => {
+		const cases = [
+			{ name: "accepts .bam extension", input: "https://s3.amazonaws.com/bucket/file.bam", expected: true },
+			{ name: "accepts local .bam", input: "file.bam", expected: true },
+			{ name: "rejects non-bam extension", input: "https://s3.amazonaws.com/bucket/file.txt", expected: false },
+			{ name: "rejects alternate extension", input: "https://example.com/path/to/file.bed", expected: false },
+		];
 
-		update = new Function(args, body);
+		it.each(cases)("$name", ({ input, expected }) => {
+			expect(check_amazon_for_bam(input)).toBe(expected);
+		});
 	});
 
-	it("generates correct XML for given form values", () => {
-		const v = {}; // dummy, not used in our $ mock
-		const result = update("", v);
-		// Check for key XML elements and values
-		expect(result).toContain('info="desc"');
-		expect(result).toContain('record_number="42"');
-		expect(result).toContain('hex_colour="#ff0000"');
-		expect(result).toContain('bam_type="Google Drive"');
-		expect(result).toContain('name="https://drive.google.com/file/d/abc"');
-		expect(result).toContain('filename="file1.bam"');
-		expect(result).toContain("<bam_exp>ctrl1</bam_exp>");
-		expect(result).toContain("<bam_exp>ctrl2</bam_exp>");
-		expect(result).toContain("<bam_exp>rep1</bam_exp>");
-		expect(result).toContain("<bam_exp>rep2</bam_exp>");
+	describe("check_links", () => {
+		const buildDom = (bamType, bamLink) => {
+			const bamInput = { id: "bam_input", value: bamLink, style: {} };
+			const bamTypeNode = { value: bamType };
+			global.document.getElementById = (id) => {
+				if (id === "Entries_all") {
+					return {
+						querySelectorAll: (selector) => {
+							if (selector === ".bam_link") return [bamInput];
+							if (selector === ".channelbamType") return [bamTypeNode];
+							return [];
+						},
+					};
+				}
+				return elementValueMap[id] || { value: "" };
+			};
+		};
+
+		const cases = [
+			{
+				name: "valid Amazon S3 bam link",
+				bamType: "Amazon AWS",
+				link: "https://s3.amazonaws.com/test/file.bam",
+				expected: true,
+			},
+			{
+				name: "valid Cyverse bam link",
+				bamType: "Amazon AWS",
+				link: "https://araport.cyverse-cdn.tacc.cloud/rnaseq/file.bam",
+				expected: true,
+			},
+			{
+				name: "Amazon link missing .bam",
+				bamType: "Amazon AWS",
+				link: "https://s3.amazonaws.com/test/file.txt",
+				expected: false,
+			},
+			{
+				name: "valid Google Drive link",
+				bamType: "Google Drive",
+				link: "https://drive.google.com/file/d/123456/view",
+				expected: true,
+			},
+			{
+				name: "invalid Google host",
+				bamType: "Google Drive",
+				link: "https://invalid.google.com/file/d/123456/view",
+				expected: false,
+			},
+			{
+				name: "unknown bam type",
+				bamType: "Unknown",
+				link: "https://example.com/file.bam",
+				expected: false,
+			},
+		];
+
+		it.each(cases)("$name", ({ bamType, link, expected }) => {
+			buildDom(bamType, link);
+			expect(check_links(".channelbamType", ".bam_link")).toBe(expected);
+		});
 	});
 });