From 077b08b5cfcfa792157e0beb04addfda88f333d1 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Mon, 6 Mar 2023 11:59:41 -0500
Subject: [PATCH] Incremental conversion of utils to typescript

---
 client/package.json                     |   2 +
 client/src/utils/{utils.js => utils.ts} | 120 ++++++++++++------------
 client/yarn.lock                        |  17 ++++
 3 files changed, 81 insertions(+), 58 deletions(-)
 rename client/src/utils/{utils.js => utils.ts} (77%)

diff --git a/client/package.json b/client/package.json
index 1d0b902aa40..6e013cd412a 100644
--- a/client/package.json
+++ b/client/package.json
@@ -142,7 +142,9 @@
     "@babel/preset-typescript": "^7.18.6",
     "@cerner/duplicate-package-checker-webpack-plugin": "^2.3.0",
     "@testing-library/jest-dom": "^5.16.4",
+    "@types/jquery": "^3.5.16",
     "@types/markdown-it": "^12.2.3",
+    "@types/underscore": "^1.11.4",
     "@typescript-eslint/eslint-plugin": "^5.51.0",
     "@typescript-eslint/parser": "^5.51.0",
     "@vue/test-utils": "^1.3.4",
diff --git a/client/src/utils/utils.js b/client/src/utils/utils.ts
similarity index 77%
rename from client/src/utils/utils.js
rename to client/src/utils/utils.ts
index 3e3a9981f48..e19d013424b 100644
--- a/client/src/utils/utils.js
+++ b/client/src/utils/utils.ts
@@ -5,21 +5,21 @@
 
 import _ from "underscore";
 import $ from "jquery";
-import { getAppRoot } from "onload/loadConfig";
-import { getGalaxyInstance } from "app";
-import _l from "utils/localization";
+import { getAppRoot } from "@/onload/loadConfig";
+import { getGalaxyInstance } from "@/app";
+import _l from "@/utils/localization";
 
 /** Builds a basic iframe */
-export function iframe(src) {
+export function iframe(src: string) {
     return `<iframe src="${src}" frameborder="0" style="width: 100%; height: 100%;"/>`;
 }
 
 /** Traverse through json */
-export function deepeach(dict, callback) {
-    for (var i in dict) {
-        var d = dict[i];
+export function deepeach(dict: any, callback: any): void {
+    for (const i in dict) {
+        const d = dict[i];
         if (_.isObject(d)) {
-            var new_dict = callback(d);
+            const new_dict = callback(d);
             if (new_dict) {
                 dict[i] = new_dict;
             }
@@ -29,29 +29,26 @@ export function deepeach(dict, callback) {
 }
 
 /** Identifies urls and replaces them with anchors */
-export function linkify(inputText) {
-    var replacedText;
-    var replacePattern1;
-    var replacePattern2;
-    var replacePattern3;
+export function linkify(inputText: string): string {
+    let replacedText;
 
     // URLs starting with http://, https://, or ftp://
-    replacePattern1 = /(\b(https?|ftp):\/\/[-A-Z0-9+&@#/%?=~_|!:,.;]*[-A-Z0-9+&@#/%=~_|])/gim;
+    const replacePattern1 = /(\b(https?|ftp):\/\/[-A-Z0-9+&@#/%?=~_|!:,.;]*[-A-Z0-9+&@#/%=~_|])/gim;
     replacedText = inputText.replace(replacePattern1, '<a href="$1" target="_blank">$1</a>');
 
     // URLs starting with "www." (without // before it, or it'd re-link the ones done above).
-    replacePattern2 = /(^|[^/])(www\.[\S]+(\b|$))/gim;
+    const replacePattern2 = /(^|[^/])(www\.[\S]+(\b|$))/gim;
     replacedText = replacedText.replace(replacePattern2, '$1<a href="http://$2" target="_blank">$2</a>');
 
     // Change email addresses to mailto:: links.
-    replacePattern3 = /(([a-zA-Z0-9\-_.])+@[a-zA-Z_]+?(\.[a-zA-Z]{2,6})+)/gim;
+    const replacePattern3 = /(([a-zA-Z0-9\-_.])+@[a-zA-Z_]+?(\.[a-zA-Z]{2,6})+)/gim;
     replacedText = replacedText.replace(replacePattern3, '<a href="mailto:$1">$1</a>');
 
     return replacedText;
 }
 
 /** Clone */
-export function clone(obj) {
+export function clone<T>(obj: T): T {
     return JSON.parse(JSON.stringify(obj) || null);
 }
 
@@ -59,7 +56,7 @@ export function clone(obj) {
  * Check if a string is a json string
  * @param{String}   text - Content to be validated
  */
-export function isJSON(text) {
+export function isJSON(text: string): boolean {
     return /^[\],:{}\s]*$/.test(
         text
             .replace(/\\["\\/bfnrtu]/g, "@")
@@ -72,7 +69,7 @@ export function isJSON(text) {
  * Sanitize/escape a string
  * @param{String}   content - Content to be sanitized
  */
-export function sanitize(content) {
+export function sanitize(content: string): string {
     return $("<div/>").text(content).html();
 }
 
@@ -81,14 +78,14 @@ export function sanitize(content) {
  * usually used for selectable options
  * @param{String}   value - Value or list to be validated
  */
-export function isEmpty(value) {
+export function isEmpty(value: any | any[]) {
     if (!(value instanceof Array)) {
         value = [value];
     }
     if (value.length === 0) {
         return true;
     }
-    for (var i in value) {
+    for (const i in value) {
         if (["__null__", "__undefined__", null, undefined].indexOf(value[i]) > -1) {
             return true;
         }
@@ -100,10 +97,10 @@ export function isEmpty(value) {
  * Convert list to pretty string
  * @param{String}   lst - List of strings to be converted in human readable list sentence
  */
-export function textify(lst) {
+export function textify(lst: string[] | string): string {
     if ($.isArray(lst)) {
         lst = lst.toString().replace(/,/g, ", ");
-        var pos = lst.lastIndexOf(", ");
+        const pos = lst.lastIndexOf(", ");
         if (pos != -1) {
             lst = `${lst.substr(0, pos)} or ${lst.substr(pos + 2)}`;
         }
@@ -121,7 +118,7 @@ export function textify(lst) {
  */
 export function get(options) {
     top.__utils__get__ = top.__utils__get__ || {};
-    var cache_key = JSON.stringify(options);
+    const cache_key = JSON.stringify(options);
     if (options.cache && top.__utils__get__[cache_key]) {
         if (options.success) {
             options.success(top.__utils__get__[cache_key]);
@@ -154,9 +151,18 @@ export function get(options) {
  * @param{Function} success - Callback on success
  * @param{Function} error   - Callback on error
  */
-export function request(options) {
+interface requestOptions {
+    type: "GET" | "POST" | "DELETE" | "PUT";
+    url: string;
+    data: any;
+    success: (response: any) => void;
+    error: (response: any, status: any) => void;
+    complete: (response: any, status: any) => void;
+}
+
+export function request(options: requestOptions) {
     // prepare ajax
-    var ajaxConfig = {
+    const ajaxConfig = {
         contentType: "application/json",
         type: options.type || "GET",
         data: options.data || {},
@@ -190,7 +196,7 @@ export function request(options) {
             }
         })
         .fail((response) => {
-            var response_text = null;
+            let response_text = null;
             try {
                 response_text = $.parseJSON(response.responseText);
             } catch (e) {
@@ -212,10 +218,10 @@ export function request(options) {
  * @param{String}   classname   - CSS class
  * @param{String}   name        - CSS property
  */
-export function cssGetAttribute(classname, name) {
-    var el = $(`<div class="${classname}"></div>`);
+export function cssGetAttribute(classname: string, name: string): string {
+    const el = $(`<div class="${classname}"></div>`);
     el.appendTo(":eq(0)");
-    var value = el.css(name);
+    const value = el.css(name);
     el.remove();
     return value;
 }
@@ -224,7 +230,7 @@ export function cssGetAttribute(classname, name) {
  * Load a CSS file
  * @param{String}   url - Url of CSS file
  */
-export function cssLoadFile(url) {
+export function cssLoadFile(url: string): void{
     if (!$(`link[href^="${url}"]`).length) {
         $(`<link href="${getAppRoot()}${url}" rel="stylesheet">`).appendTo("head");
     }
@@ -244,33 +250,33 @@ export function merge(options, optionsDefault) {
 }
 
 /**
- * Round floaing point 'number' to 'numPlaces' number of decimal places.
- * @param{Object}   number      a floaing point number
- * @param{Object}   numPlaces   number of decimal places
+ * Round floating point 'number' to 'numPlaces' number of decimal places.
+ * @param{number}   number      a floaing point number
+ * @param{number}   numPlaces   number of decimal places
  */
-export function roundToDecimalPlaces(number, numPlaces) {
-    var placesMultiplier = 1;
-    for (var i = 0; i < numPlaces; i++) {
+export function roundToDecimalPlaces(number: number, numPlaces: number) {
+    let placesMultiplier = 1;
+    for (const i = 0; i < numPlaces; i++) {
         placesMultiplier *= 10;
     }
     return Math.round(number * placesMultiplier) / placesMultiplier;
 }
 
 // calculate on import
-var kb = 1024;
-var mb = kb * kb;
-var gb = mb * kb;
-var tb = gb * kb;
+const kb = 1024;
+const mb = kb * kb;
+const gb = mb * kb;
+const tb = gb * kb;
 
 /**
  * Format byte size to string with units
  * @param{Integer}   size           - Size in bytes
  * @param{Boolean}   normal_font    - Switches font between normal and bold
  */
-export function bytesToString(size, normal_font, numberPlaces) {
+export function bytesToString(size: number, normal_font: boolean, numberPlaces: number) {
     numberPlaces = numberPlaces !== undefined ? numberPlaces : 1;
     // identify unit
-    var unit = "";
+    let unit = "";
     if (size >= tb) {
         size = size / tb;
         unit = "TB";
@@ -289,7 +295,7 @@ export function bytesToString(size, normal_font, numberPlaces) {
         return normal_font ? "0 b" : "<strong>-</strong>";
     }
     // return formatted string
-    var rounded = unit == "b" ? size : roundToDecimalPlaces(size, numberPlaces);
+    const rounded = unit == "b" ? size : roundToDecimalPlaces(size, numberPlaces);
     if (normal_font) {
         return `${rounded} ${unit}`;
     } else {
@@ -298,16 +304,16 @@ export function bytesToString(size, normal_font, numberPlaces) {
 }
 
 /** Create a unique id */
-export function uid() {
+export function uid(): string {
     top.__utils__uid__ = top.__utils__uid__ || 0;
     return `uid-${top.__utils__uid__++}`;
 }
 
 /** Create a time stamp */
-export function time() {
-    var d = new Date();
-    var hours = (d.getHours() < 10 ? "0" : "") + d.getHours();
-    var minutes = (d.getMinutes() < 10 ? "0" : "") + d.getMinutes();
+export function time(): string {
+    const d = new Date();
+    const hours = (d.getHours() < 10 ? "0" : "") + d.getHours();
+    const minutes = (d.getMinutes() < 10 ? "0" : "") + d.getMinutes();
     return `${d.getDate()}/${d.getMonth() + 1}/${d.getFullYear()}, ${hours}:${minutes}`;
 }
 
@@ -324,7 +330,7 @@ export function appendScriptStyle(data) {
 }
 
 /** Get querystrings from url */
-export function getQueryString(key) {
+export function getQueryString(key: string): string {
     return decodeURIComponent(
         window.location.search.replace(
             new RegExp(`^(?:.*[&\\?]${encodeURIComponent(key).replace(/[.+*]/g, "\\$&")}(?:\\=([^&]*))?)?.*$`, "i"),
@@ -333,7 +339,7 @@ export function getQueryString(key) {
     );
 }
 
-export function setWindowTitle(title) {
+export function setWindowTitle(title: string): void {
     const Galaxy = getGalaxyInstance();
     if (title) {
         window.document.title = `Galaxy ${Galaxy.config.brand ? ` | ${Galaxy.config.brand}` : ""} | ${_l(title)}`;
@@ -350,12 +356,10 @@ export function setWindowTitle(title) {
  * @param {string} str the input value
  * @returns {integer}
  */
-export function hashFnv32a(str) {
-    var i;
-    var l;
-    var hval = 0x811c9dc5;
+export function hashFnv32a(str: string): number {
+    let hval = 0x811c9dc5;
 
-    for (i = 0, l = str.length; i < l; i++) {
+    for (const i = 0, l = str.length; i < l; i++) {
         hval ^= str.charCodeAt(i);
         hval += (hval << 1) + (hval << 4) + (hval << 7) + (hval << 8) + (hval << 24);
     }
@@ -376,9 +380,9 @@ export async function waitForElementToBePresent(selector) {
 
 /**
  * Delays the next operation the specified amount of time.
- * @param {Number} delayInMilliseconds The amount of time to wait in milliseconds
+ * @param {number} delayInMilliseconds The amount of time to wait in milliseconds
  */
-export async function delay(delayInMilliseconds) {
+export async function delay(delayInMilliseconds: number) {
     if (delayInMilliseconds > 0) {
         await new Promise((r) => setTimeout(r, delayInMilliseconds));
     }
diff --git a/client/yarn.lock b/client/yarn.lock
index 1255f88aa4b..0abe3f6abc9 100644
--- a/client/yarn.lock
+++ b/client/yarn.lock
@@ -2334,6 +2334,13 @@
     jest-matcher-utils "^28.0.0"
     pretty-format "^28.0.0"
 
+"@types/jquery@^3.5.16":
+  version "3.5.16"
+  resolved "https://registry.yarnpkg.com/@types/jquery/-/jquery-3.5.16.tgz#632131baf30951915b0317d48c98e9890bdf051d"
+  integrity sha512-bsI7y4ZgeMkmpG9OM710RRzDFp+w4P1RGiIt30C1mSBT+ExCleeh4HObwgArnDFELmRrOpXgSYN9VF1hj+f1lw==
+  dependencies:
+    "@types/sizzle" "*"
+
 "@types/jsdom@^20.0.0":
   version "20.0.1"
   resolved "https://registry.yarnpkg.com/@types/jsdom/-/jsdom-20.0.1.tgz#07c14bc19bd2f918c1929541cdaacae894744808"
@@ -2436,6 +2443,11 @@
     "@types/mime" "*"
     "@types/node" "*"
 
+"@types/sizzle@*":
+  version "2.3.3"
+  resolved "https://registry.yarnpkg.com/@types/sizzle/-/sizzle-2.3.3.tgz#ff5e2f1902969d305225a047c8a0fd5c915cebef"
+  integrity sha512-JYM8x9EGF163bEyhdJBpR2QX1R5naCJHC8ucJylJ3w9/CVBaskdQ8WqBf8MmQrd1kRvp/a4TS8HJ+bxzR7ZJYQ==
+
 "@types/sockjs@^0.3.33":
   version "0.3.33"
   resolved "https://registry.npmjs.org/@types/sockjs/-/sockjs-0.3.33.tgz"
@@ -2475,6 +2487,11 @@
   resolved "https://registry.yarnpkg.com/@types/tough-cookie/-/tough-cookie-4.0.2.tgz#6286b4c7228d58ab7866d19716f3696e03a09397"
   integrity sha512-Q5vtl1W5ue16D+nIaW8JWebSSraJVlK+EthKn7e7UcD4KWsaSJ8BqGPXNaPghgtcn/fhvrN17Tv8ksUsQpiplw==
 
+"@types/underscore@^1.11.4":
+  version "1.11.4"
+  resolved "https://registry.yarnpkg.com/@types/underscore/-/underscore-1.11.4.tgz#62e393f8bc4bd8a06154d110c7d042a93751def3"
+  integrity sha512-uO4CD2ELOjw8tasUrAhvnn2W4A0ZECOvMjCivJr4gA9pGgjv+qxKWY9GLTMVEK8ej85BxQOocUyE7hImmSQYcg==
+
 "@types/web-bluetooth@^0.0.16":
   version "0.0.16"
   resolved "https://registry.yarnpkg.com/@types/web-bluetooth/-/web-bluetooth-0.0.16.tgz#1d12873a8e49567371f2a75fe3e7f7edca6662d8"