Fix XML generator not generating XMLs (#45)

Fix an issue where the XML generator was not allowing the generation of
XMLs due to issue with link checking.

In addition:

- Fixed unit tests not properly testing source files
- Add a minification `package.json` script to more reliable minify the
JS and CSS files
- Removed the unnecessary `py-test` and `py-clean`  in the `Makefile`

Author: AlexJSully

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

@@ -292,7 +292,7 @@ function correct_ReadMapCount(class_name) {
 
 	for (const element of x) {
 		element.value = element.value.trim();
-		if (element.value === ("" || null || undefined)) {
+		if (!element.value) {
 			element.value = 0;
 		}
 		element.value = only_ReadNum(element.value);
@@ -326,55 +326,46 @@ function only_ReadNum(input_string) {
 function check_links(bam_name, repo_name) {
 	const x = document.getElementById("Entries_all").querySelectorAll(repo_name);
 	const bam_x = document.getElementById("Entries_all").querySelectorAll(bam_name);
+	let foundBamInput = false;
+
 	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);
-
-					if (
-						(urlString.host("s3.amazonaws.com") || x[i].value.includes("araport.cyverse-cdn.tacc.cloud")) &&
-						check_amazon_for_bam(x[i].value)
-					) {
-						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;
-					}
-				} else {
+			foundBamInput = true;
+			if (!x[i].value || !bam_x?.[i]?.value) {
+				return false;
+			}
+
+			let urlString;
+			try {
+				urlString = new URL(x[i].value);
+			} catch {
+				return false;
+			}
+
+			const hostValue = urlString?.host ?? "";
+			const bamHostType = bam_x[i].value;
+
+			if (bamHostType === "Google Drive") {
+				if (!["drive.google.com", "www.drive.google.com"].includes(hostValue)) {
+					return false;
+				}
+			} else if (bamHostType === "Amazon AWS") {
+				if (
+					!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 false;
 				}
 			} else {
 				return false;
 			}
 		}
 	}
+
+	return foundBamInput;
 }
 
 /**
@@ -507,19 +498,21 @@ 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 +521,7 @@ 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 +1293,12 @@ 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,
+	};
+}