Merge resolution branch into biorepo master

.vscode/launch.json

@@ -0,0 +1,48 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+        {
+            "name": "Listen for Xdebug",
+            "type": "php",
+            "request": "launch",
+            "port": 9003
+        },
+        {
+            "name": "Launch currently open script",
+            "type": "php",
+            "request": "launch",
+            "program": "${file}",
+            "cwd": "${fileDirname}",
+            "port": 0,
+            "runtimeArgs": [
+                "-dxdebug.start_with_request=yes"
+            ],
+            "env": {
+                "XDEBUG_MODE": "debug,develop",
+                "XDEBUG_CONFIG": "client_port=${port}"
+            }
+        },
+        {
+            "name": "Launch Built-in web server",
+            "type": "php",
+            "request": "launch",
+            "runtimeArgs": [
+                "-dxdebug.mode=debug",
+                "-dxdebug.start_with_request=yes",
+                "-S",
+                "localhost:0"
+            ],
+            "program": "",
+            "cwd": "${workspaceRoot}",
+            "port": 9003,
+            "serverReadyAction": {
+                "pattern": "Development Server \\(http://localhost:([0-9]+)\\) started",
+                "uriFormat": "http://localhost:%s",
+                "action": "openExternally"
+            }
+        }
+    ]
+}

README.md

@@ -33,6 +33,7 @@ Symbiota has been generously funded by the National Science Foundation (DBI-0743
 
 - Tested thoroughly on Linux and Windows operating systems
 - Code should work with an PHP enabled web server, though central development and testing done using Apache HTTP Server
+- Development and testing preformed using MariaDB. If you are using Oracle MySQL instead, please [report any issues](https://github.com/BioKIC/Symbiota/issues/new).
 
 ## INSTALLATION
 

accessibility/module.php

@@ -0,0 +1,43 @@
+<?php
+if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT.'/content/lang/templates/accessibility.' . $LANG_TAG . '.php'))
+	include_once($SERVER_ROOT . '/content/lang/templates/accessibility.en.php');
+else include_once($SERVER_ROOT . '/content/lang/templates/accessibility.' . $LANG_TAG . '.php');
+?>
+<dialog id="accessibility-modal" class="accessibility-dialog" aria-label="<?= $LANG['A_ACCESSIBILITY_OPTIONS']; ?>">
+	<h1><?= $LANG['A_ACCESSIBILITY_OPTIONS']; ?></h1>
+	<p class="bottom-breathing-room-rel"><?= $LANG['A_ACCESSIBILITY_OPTIONS_DESCRIPTION']; ?></p>
+	<button type="button" class="btn btn-primary bottom-breathing-room-rel" onclick="toggleAccessibilityStyles()" id="accessibility-button" data-accessibility="accessibility-button">
+		<?= $LANG['A_TOGGLE_508_ON'] ?>
+	</button>
+	<form method="dialog">
+		<button type="submit" class="btn btn-primary"><?= $LANG['A_CLOSE']; ?></button>
+	</form>
+</dialog>
+<button id="accessibility-options-button" type="button" class="btn btn-primary  accessibility-option-button">
+	<span class="button__item-container">
+		<?= $LANG['A_ACCESSIBILITY_OPTIONS']; ?>
+		<span>
+			<img alt="<?= $LANG['A_ACCESSIBILITY_ICON'] ?>" src="<?= $CLIENT_ROOT ?>/images/accessibility_FILL0_wght400_GRAD0_opsz24.svg" />
+		</span>
+	</span>
+</button>
+<script type="text/javascript">
+	const toggleOff508Text = "<?= $LANG['A_TOGGLE_508_OFF'] ?>";
+	const toggleOn508Text = "<?= $LANG['A_TOGGLE_508_ON'] ?>";
+	const clientRootPath = "<?= $CLIENT_ROOT ?>";
+</script>
+<link href="<?= $CSS_BASE_PATH ?>/symbiota/accessibility-controls.css?ver=<?= $CSS_VERSION ?>" type="text/css" rel="stylesheet">
+<?php
+if($ACCESSIBILITY_ACTIVE){
+	?>
+	<link href="<?= $CSS_BASE_PATH ?>/symbiota/accessibility-compliant.css?ver=<?= $CSS_VERSION ?>" type="text/css" rel="stylesheet" data-accessibility-link="accessibility-css-link" >
+	<link href="<?= $CSS_BASE_PATH ?>/symbiota/condensed.css?ver=<?= $CSS_VERSION ?>" type="text/css" rel="stylesheet" data-accessibility-link="accessibility-css-link" disabled >
+	<?php
+} else{
+	?>
+	<link href="<?= $CSS_BASE_PATH ?>/symbiota/accessibility-compliant.css?ver=<?= $CSS_VERSION ?>" type="text/css" rel="stylesheet" data-accessibility-link="accessibility-css-link" disabled >
+	<link href="<?= $CSS_BASE_PATH ?>/symbiota/condensed.css?ver=<?= $CSS_VERSION ?>" type="text/css" rel="stylesheet" data-accessibility-link="accessibility-css-link" >
+	<?php
+}
+?>
+<script src="<?= $CLIENT_ROOT ?>/js/symb/accessibilityUtils.js?ver=1b" type="text/javascript"></script>

accessibility/rpc/toggle-styles.php

@@ -0,0 +1,13 @@
+<?php
+include_once('../../config/symbini.php');
+$currentlyEnabledStylesheet = $_REQUEST['currentEnabledStylesheet'];
+//session_start();
+$accessiblePath = $CSS_BASE_PATH . '/symbiota/condensed.css?ver=14';
+$condensedPath = $CSS_BASE_PATH . '/symbiota/accessibility-compliant.css?ver=14';
+if($currentlyEnabledStylesheet === $condensedPath){
+    $_SESSION['active_stylesheet'] = $accessiblePath;
+} else{
+    $_SESSION['active_stylesheet'] = $condensedPath;
+}
+echo $_SESSION['active_stylesheet'];
+?>

admin/index.php

@@ -1,11 +1,13 @@
 <?php
 include_once('../config/symbini.php');
+if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT.'/content/lang/prohibit.'.$LANG_TAG.'.php')) include_once($SERVER_ROOT.'/content/lang/prohibit.en.php');
+else include_once($SERVER_ROOT.'/content/lang/prohibit.'.$LANG_TAG.'.php');
 header("Content-Type: text/html; charset=".$CHARSET);
 header("Location: ".$CLIENT_ROOT."/index.php");
 ?>
-<html>
+<html lang="en">
 	<head>
-		<title>Forbidden</title>
+		<title><?php echo $LANG['FORBIDDEN']; ?></title>
 		<?php
 		include_once($SERVER_ROOT.'/includes/head.php');
 		?>
@@ -15,13 +17,13 @@
 		$displayLeftMenu = true;
 		include($SERVER_ROOT.'/includes/header.php');
 		?>
-		<div id="innertext">
-			<h1>Forbidden</h1>
+		<div role="main" id="innertext">
+			<h1><?php echo $LANG['FORBIDDEN']; ?></h1>
 			<div style="font-weight:bold;">
-				You don't have permission to access this page.
+				<?php echo $LANG['NO_PERMISSION']; ?>
 			</div>
 			<div style="font-weight:bold;margin:10px;">
-				<a href="<?php echo $CLIENT_ROOT; ?>/index.php">Return to index page</a>
+				<a href="<?php echo htmlspecialchars($CLIENT_ROOT, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE); ?>/index.php"><?php echo $LANG['RETURN']; ?></a>
 			</div>
 		</div>
 		<?php

admin/portalindex.php

@@ -16,15 +16,15 @@
 $isEditor = 0;
 if($IS_ADMIN) $isEditor = 1;
 ?>
-<html>
+<html lang="en">
 	<head>
 		<title><?php echo $DEFAULT_TITLE; ?> Portal Index Control Panel</title>
 		<link href="<?php echo $CSS_BASE_PATH; ?>/jquery-ui.css" type="text/css" rel="stylesheet">
 		<?php
 		include_once($SERVER_ROOT.'/includes/head.php');
 		?>
-		<script src="<?php echo $CLIENT_ROOT; ?>/js/jquery.js" type="text/javascript"></script>
-		<script src="<?php echo $CLIENT_ROOT; ?>/js/jquery-ui.js" type="text/javascript"></script>
+		<script src="<?php echo $CLIENT_ROOT; ?>/js/jquery-3.7.1.min.js" type="text/javascript"></script>
+		<script src="<?php echo $CLIENT_ROOT; ?>/js/jquery-ui.min.js" type="text/javascript"></script>
 		<script type="text/javascript">
 			function validateHandshakeForm(f){
 				if(f.remotePath.value == ""){
@@ -52,7 +52,7 @@ function validateHandshakeForm(f){
 			<a href="../../index.php">Home</a> &gt;&gt;
 			<b><a href="portalindex.php">Portal Index Control Panel</a></b>
 		</div>
-		<div id="innertext">
+		<div role="main" id="innertext">
 			<?php
 			if(!isset($GLOBALS['ACTIVATE_PORTAL_INDEX'])){
 				echo 'This feature has not yet been activated within this portal';
@@ -62,8 +62,8 @@ function validateHandshakeForm(f){
 					echo '<fieldset>';
 					echo '<legend>Action Panel</legend>';
 					if($formSubmit == 'importProfile'){
-						if($collid = $portalManager->importProfile($portalID, $remoteID)) echo '<div><a href="../collections/misc/collprofiles.php?collid='.$collid.'" target="_blank">New snapshot collection created</a></div>';
-						else echo '<div>failed to insert new collections: '.$portalManager->getErrorMessage().'</div>';
+						if($collid = $portalManager->importProfile($portalID, $remoteID)) echo '<div><a href="../collections/misc/collprofiles.php?collid=' . htmlspecialchars($collid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '" target="_blank">New snapshot collection created</a></div>';
+						else echo '<div>failed to insert new collections: ' . $portalManager->getErrorMessage() . '</div>';
 					}
 					elseif($formSubmit == 'initiateHandshake'){
 						if($resArr = $portalManager->initiateHandshake($remotePath)){
@@ -89,7 +89,7 @@ function validateHandshakeForm(f){
 						<div class="handshake-div"><a href="#" onclick="$('.handshake-div').toggle(); return false;">Initiate Handshake with External Portal</a></div>
 						<div class="handshake-div" style="display:none">
 							<form action="portalindex.php" method="post" onsubmit="return validateHandshakeForm(this)">
-								<div class="field-row"><label>Path to Remote Portal:</label> <input name="remotePath" type="text" value="<?php echo $remotePath; ?>" style="width: 500px" /></div>
+								<div class="field-row"><label for="remotePath">Path to Remote Portal</label> <input name="remotePath" id="remotePath" type="text" value="<?php echo $remotePath; ?>" style="width: 500px" /></div>
 								<div class="field-row"><button name="formsubmit" type="submit" value="initiateHandshake">Initiate Handshake</button></div>
 							</form>
 						</div>
@@ -108,7 +108,7 @@ function validateHandshakeForm(f){
 								$href = '';
 								if($fieldName=='urlRoot') $href = $fieldValue;
 								elseif($fieldName=='guid') $href = $portalArr['urlRoot'].'/api/v2/installation/ping';
-								if($href) echo '<a href="'.$href.'" target="_blank">';
+								if($href) echo '<a href="' . htmlspecialchars($href, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '" target="_blank">';
 								echo $fieldValue;
 								if($href) echo '</a>';
 								echo '</div>';
@@ -130,7 +130,7 @@ function validateHandshakeForm(f){
 								}
 							}
 							$remoteUrl = $portalArr['urlRoot'].'/collections/misc/collprofiles.php?collid='.$remoteCollid;
-							echo '<div><label>Remote collection</label>: <a href="'.$remoteUrl.'" target="_blank">'.$remoteUrl.'</a></div>';
+							echo '<div><label>Remote collection</label>: <a href="' . htmlspecialchars($remoteUrl, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '" target="_blank">' . htmlspecialchars($remoteUrl, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '</a></div>';
 							if($internalArr){
 								echo '<fieldset>';
 								echo '<legend>Internally Mapped Snapshot Collection</legend>';
@@ -139,7 +139,7 @@ function validateHandshakeForm(f){
 									echo '<div><label>Specimen count</label>: '.number_format($intArr['recordCnt']).'</div>';
 									echo '<div><label>Refresh date</label>: '.$intArr['uploadDate'].'</div>';
 									$internalUrl = $CLIENT_ROOT.'/collections/misc/collprofiles.php?collid='.$collid;
-									echo '<div><label>Internal collection</label>: <a href="'.$internalUrl.'" target="_blank">'.$internalUrl.'</a></div>';
+									echo '<div><label>Internal collection</label>: <a href="' . htmlspecialchars($internalUrl, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '" target="_blank">' . htmlspecialchars($internalUrl, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '</a></div>';
 									if($importProfile = $portalManager->getDataImportProfile($collid)){
 										foreach($importProfile as $uspid => $profileArr){
 											echo '<hr/>';
@@ -148,8 +148,8 @@ function validateHandshakeForm(f){
 											echo '<div><label>Path</label>: '.$profileArr['path'].'</div>';
 											echo '<div><label>Query string</label>: '.$profileArr['queryStr'].'</div>';
 											echo '<div><label>Stored procedure (cleaning)</label>: '.$profileArr['cleanUpSp'].'</div>';
-											echo '<div>Display all <a href="../collections/admin/specuploadmanagement.php?collid='.$collid.'" target="_blank">Import Profiles</a></div>';
-											echo '<div>Initiate <a href="../collections/admin/specuploadmap.php?uploadtype=13&uspid='.$uspid.'&collid='.$collid.'" target="_blank">Data Import</a></div>';
+											echo '<div>Display all <a href="../collections/admin/specuploadmanagement.php?collid=' . htmlspecialchars($collid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '" target="_blank">Import Profiles</a></div>';
+											echo '<div>Initiate <a href="../collections/admin/specuploadmap.php?uploadtype=13&uspid=' . htmlspecialchars($uspid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '&collid=' . htmlspecialchars($collid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '" target="_blank">Data Import</a></div>';
 											echo '</div>';
 										}
 									}
@@ -176,14 +176,14 @@ function validateHandshakeForm(f){
 								echo '<tr><th>ID</th><th>Institution Code</th><th>Collection Code</th><th>Collection Name</th><th>Dataset Type</th><th>Management</th><th>Mapped Internally</th></tr>';
 								foreach($collList as $collArr){
 									echo '<tr>';
-									echo '<td><a href="portalindex.php?portalid='.$portalID.'&remoteid='.$collArr['collID'].'">'.$collArr['collID'].'</a></td>';
+									echo '<td><a href="portalindex.php?portalid=' . htmlspecialchars($portalID, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '&remoteid=' . htmlspecialchars($collArr['collID'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '">' . htmlspecialchars($collArr['collID'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '</a></td>';
 									echo '<td>'.$collArr['institutionCode'].'</td>';
 									echo '<td>'.$collArr['collectionCode'].'</td>';
 									echo '<td>'.$collArr['collectionName'].'</td>';
 									echo '<td>'.$collArr['collType'].'</td>';
 									echo '<td>'.$collArr['managementType'].'</td>';
 									if(isset($collArr['internal']) && $collArr['internal'])
-										$internal = '<a href="'.$CLIENT_ROOT.'/collections/misc/collprofiles.php?collid='.key($collArr['internal']).'" target="_blank">Yes</a>';
+										$internal = '<a href="' . htmlspecialchars($CLIENT_ROOT, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '/collections/misc/collprofiles.php?collid=' . htmlspecialchars(key($collArr['internal']), ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '" target="_blank">Yes</a>';
 									else $internal = 'No';
 									echo '<td>'.$internal.'</td>';
 									echo '</tr>';
@@ -215,4 +215,4 @@ function validateHandshakeForm(f){
 		include($SERVER_ROOT.'/includes/footer.php');
 		?>
 	</body>
-</html>
+</html>