Finished downloads + workflows page

Downloads.php

@@ -0,0 +1,43 @@
+<?php
+require 'header.php';
+require 'navbar.php';
+session_start();
+if(empty($_SESSION['moduleFileCreated'])) {
+    $_SESSION['moduleFileCreated'] = false;
+}
+if(empty($_SESSION['inputFileCreated'])) {
+    $_SESSION['inputFileCreated'] = false;
+}
+?>
+<br>
+<div class="container">
+    <div class="card">
+        <div class="card-body">
+            <div>
+                <h5>Default Build</h5>
+                <form method="get" action="scripts/defaultBuild.php">
+                    <button class="btn btn-secondary" type="submit">Download</button>
+                </form>
+            </div>
+            <?php if ($_SESSION['inputFileCreated']): ?>
+            <hr>
+            <div>
+                <h5>Input File</h5>
+                <form method="get" action="scripts/userInputFile.php">
+                    <button class="btn btn-secondary" type="submit">Download</button>
+                </form>
+            </div>
+            <?php endif; ?>
+            <?php if ($_SESSION['moduleFileCreated']): ?>
+            <hr>
+            <div>
+                <h5>Module File With User-Added Modules</h5>
+                <form method="get" action="scripts/userModuleFile.php">
+                    <button class="btn btn-secondary" type="submit">Download</button>
+                </form>
+            </div>
+            <?php endif; ?>
+        </div>
+    </div>
+
+</div>

Modules.php

@@ -7,10 +7,10 @@
  */
 require 'header.php';
 require 'navbar.php';
-require 'Module.php';
+require './models/Module.php';
 session_start();
 $userModule = null;
-require 'addModule.php';
+require './scripts/addModule.php';
 
 $xml = simplexml_load_file("module.xml") or die("Error: Cannot create xml object.");
 $modules = array();

Workflows.php

@@ -1,9 +1,9 @@
 <?php
 require 'header.php';
 require 'navbar.php';
-require 'Module.php';
+require './models/Module.php';
 session_start();
-require 'createInputFile.php';
+require './scripts/createInputFile.php';
 
 $xml = simplexml_load_file("module.xml") or die("Error: Cannot create xml object.");
 $modules = array();
@@ -50,7 +50,7 @@
                 </div>
                 <div class="form-group">
                     <label for="outputFolder">Output Folder</label>
-                    <input type="text" class="form-control" name="outputFolder" id="outputFolder">
+                    <input type="text" class="form-control" name="outputFolder" placeholder="Output Folder" id="outputFolder">
                 </div>
                 <div class="input-group mb-3">
                     <select class="form-control" id="moduleSelect">
@@ -132,7 +132,7 @@ function setButtonDisabledIfInvalid() {
         const uniqueID = $("#uniqueId").val();
         const outputFolder = $("#outputFolder").val();
         const workflowStr = createWorkflowString();
-        $.get("./moduleList.php", function (data) {
+        $.get("./scripts/moduleList.php", function (data) {
             const parsedData = JSON.parse(data);
             workflow.map( module => {
                 for (let i = 0; i < parsedData.length; i++) {

header.php

@@ -5,7 +5,7 @@
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <title>Bioliner</title>
     <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
-    <link rel="stylesheet" href="./styles.css">
+    <link rel="stylesheet" href="../styles.css">
     <script src="https://code.jquery.com/jquery-3.3.1.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
     <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
     <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>

index.php

@@ -1,6 +1,6 @@
 <?php
-require 'header.php';
-require 'navbar.php';
+require './header.php';
+require './navbar.php';
 ?>
 <div class="container">
     <h4>Welcome to Bioliner.</h4>

navbar.php

@@ -1,12 +1,13 @@
 <nav class="navbar navbar-expand-lg navbar-light bg-light">
-    <a class="navbar-brand" href="./index.php">Bioliner</a>
+    <a class="navbar-brand" href="/index.php">Bioliner</a>
     <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarNavAltMarkup" aria-controls="navbarNavAltMarkup" aria-expanded="false" aria-label="Toggle navigation">
         <span class="navbar-toggler-icon"></span>
     </button>
     <div class="collapse navbar-collapse" id="navbarNavAltMarkup">
         <div class="navbar-nav">
-            <a class="nav-item nav-link" href="./Modules.php">Modules</a>
-            <a class="nav-item nav-link" href="./Workflows.php">Workflows</a>
+            <a class="nav-item nav-link" href="/views/Modules.php">Modules</a>
+            <a class="nav-item nav-link" href="/views/Workflows.php">Workflows</a>
+            <a class="nav-item nav-link" href="/views/Downloads.php">Downloads</a>
         </div>
     </div>
 </nav>

addModule.php → scripts/addModule.php

@@ -16,7 +16,7 @@
     if(!file_exists($target_dir)) {
         mkdir($target_dir);
     }
-    
+
     $userModuleFile = $target_dir . "module.xml";
     $_SESSION["userModules"][] = $userModule;
     // If they have already added a module, append to that file.

scripts/defaultBuild.php

@@ -0,0 +1,22 @@
+<?php
+session_start();
+$file = "../zip-files/bioliner.zip";
+$rootPath = realpath("../zip-files/bioliner.zip");
+
+if (file_exists($rootPath) && is_file($rootPath)) {
+
+    header('Content-Description: File Transfer');
+    header("Content-Type: application/zip");
+    header('Content-Disposition: attachment; filename="'.basename($rootPath).'"');
+    header('Expires: 0');
+    header('Cache-Control: must-revalidate');
+    header('Pragma: public');
+    header('Content-Length: ' . filesize($rootPath));
+    if (ob_get_level()) {
+        ob_end_clean();
+    }
+    readfile($file);
+    exit;
+} else {
+    echo "Invalid file";
+}

scripts/userInputFile.php

@@ -0,0 +1,20 @@
+<?php
+session_start();
+$inputFile = "../uploads" . DIRECTORY_SEPARATOR . session_id() . DIRECTORY_SEPARATOR . "input.xml";
+if (file_exists($inputFile) && is_file($inputFile)) {
+
+    header('Content-Description: File Transfer');
+    header('Content-Type: application/octet-stream');
+    header('Content-Disposition: attachment; filename="'.basename($inputFile).'"');
+    header('Expires: 0');
+    header('Cache-Control: must-revalidate');
+    header('Pragma: public');
+    header('Content-Length: ' . filesize($inputFile));
+    if (ob_get_level()) {
+        ob_end_clean();
+    }
+    readfile($inputFile);
+    exit;
+} else {
+    echo "Error downloading file";
+}

scripts/userModuleFile.php

@@ -0,0 +1,20 @@
+<?php
+session_start();
+$inputFile = "../uploads" . DIRECTORY_SEPARATOR . session_id() . DIRECTORY_SEPARATOR . "module.xml";
+if (file_exists($inputFile) && is_file($inputFile)) {
+
+    header('Content-Description: File Transfer');
+    header('Content-Type: application/octet-stream');
+    header('Content-Disposition: attachment; filename="'.basename($inputFile).'"');
+    header('Expires: 0');
+    header('Cache-Control: must-revalidate');
+    header('Pragma: public');
+    header('Content-Length: ' . filesize($inputFile));
+    if (ob_get_level()) {
+        ob_end_clean();
+    }
+    readfile($inputFile);
+    exit;
+} else {
+    echo "Error downloading file";
+}