Merge pull request #508 from BioKIC/temp_resolve_conflict

Update from BioKIC Development
BioKIC · Aug 6, 2024 · 6be4e28 · 6be4e28
2 parents 2c015f0 + 351a9c8
commit 6be4e28
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Showing 112 changed files with 1,131 additions and 982 deletions.
diff --git a/checklists/clgmap.php b/checklists/clgmap.php
@@ -1,18 +1,11 @@
 <?php
 include_once('../config/symbini.php');
 include_once($SERVER_ROOT.'/classes/ChecklistManager.php');
-if($LANG_TAG != 'en' && file_exists($SERVER_ROOT.'/content/lang/checklists/clgmap.' . $LANG_TAG . '.php')) include_once($SERVER_ROOT . '/content/lang/checklists/clgmap.' . $LANG_TAG . '.php');
-else include_once($SERVER_ROOT.'/content/lang/checklists/clgmap.en.php');
-if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT.'/content/lang/header.' . $LANG_TAG . '.php')) include_once($SERVER_ROOT . '/content/lang/header.en.php');
-else include_once($SERVER_ROOT . '/content/lang/header.' . $LANG_TAG . '.php');
+if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT.'/content/lang/checklists/clgmap.' . $LANG_TAG . '.php')) include_once($SERVER_ROOT . '/content/lang/checklists/clgmap.en.php');
+else include_once($SERVER_ROOT.'/content/lang/checklists/clgmap.' . $LANG_TAG . '.php');
 header("Content-Type: text/html; charset=".$CHARSET);
 
-$pid = $_REQUEST['pid'];
-$target = array_key_exists('target',$_REQUEST)?$_REQUEST['target']:'checklists';
-
-//Sanitation
-$pid = htmlspecialchars($pid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE);
-if(!is_numeric($pid)) $pid = 0;
+$pid = filter_var($_REQUEST['pid'], FILTER_SANITIZE_NUMBER_INT);
 
 $clManager = new ChecklistManager();
 $clManager->setProj($pid);
@@ -22,11 +15,11 @@
 <!DOCTYPE html>
 <html lang="<?php echo $LANG_TAG ?>">
    <head>
-      <?php
-        include_once($SERVER_ROOT.'/includes/leafletMap.php');
-	     include_once($SERVER_ROOT.'/includes/googleMap.php');
-      ?>
-		<title><?php echo $DEFAULT_TITLE.' - '.(isset($LANG['H_INVENTORIES'])?$LANG['H_INVENTORIES']:'Species Checklists'); ?></title>
+		<?php
+		include_once($SERVER_ROOT.'/includes/leafletMap.php');
+		include_once($SERVER_ROOT.'/includes/googleMap.php');
+		?>
+		<title><?= $DEFAULT_TITLE . ' - ' . $LANG['TITLE'] ?></title>
 
 		<script type="text/javascript">
 
@@ -48,7 +41,7 @@ function leafletInit() {
                markers.push(L.marker(latlng)
                   .bindTooltip(checklist.name)
                   .bindPopup(`<div style=\'width:300px;\'>
-                     <b>${checklist.name}</b><br/><?php echo (isset($LANG['DOUBLE_CLICK'])?$LANG['DOUBLE_CLICK']:'Double Click to open'); ?>
+                     <b>${checklist.name}</b><br/><?= $LANG['DOUBLE_CLICK'] ?>
                      </div>`)
                   .on('dblclick', () => navigateToCheckList(checklistId, pid)));
             }
@@ -81,7 +74,7 @@ function closeAllInfoWins(){
                })
                const infoWin = new google.maps.InfoWindow({
                   content: `<div style=\'width:300px;\'>
-                     <b>${checklist.name}</b><br/><?php echo (isset($LANG['DOUBLE_CLICK'])?$LANG['DOUBLE_CLICK']:'Double Click to open'); ?>
+                     <b>${checklist.name}</b><br/><?= $LANG['DOUBLE_CLICK'] ?>
                   </div>`
                });
 
@@ -109,7 +102,7 @@ function initialize(){
                pid = data.getAttribute('data-pid');
                checklists = JSON.parse(data.getAttribute('data-checklists'));
             } catch (err) {
-               alert("<?php echo (isset($LANG['FAILED_TO_LOAD'])?$LANG['FAILED_TO_LOAD']:'Failed to load checklist data'); ?>");
+               alert("<?= $LANG['FAILED_TO_LOAD'] ?>");
             }
 
             <?php if(empty($GOOGLE_MAP_KEY)) { ?>
@@ -126,24 +119,21 @@ function initialize(){
 				margin: 0;
 				padding: 0;
 			}
-         .screen-reader-only {
+			.screen-reader-only {
 				position: absolute;
 				left: -10000px;
 			}
 		</style>
 	</head>
 	<body style="background-color:#ffffff;" onload="initialize()">
-      <?php
-			// if($shouldUseMinimalMapHeader) include_once($SERVER_ROOT . '/includes/minimalheader.php');
+		<?php
+		// if($shouldUseMinimalMapHeader) include_once($SERVER_ROOT . '/includes/minimalheader.php');
 		?>
-      <h1 class="page-heading screen-reader-only" style="margin-top:30px;">Checklist Map</h1>
+		<h1 class="page-heading screen-reader-only" style="margin-top:30px;">Checklist Map</h1>
 		<div id="map_canvas"></div>
-      <div
-        id="service-container"
-        class="service-container"
-        data-checklists="<?= htmlspecialchars(json_encode($clManager->getResearchPoints()))?>"
-        data-pid="<?= htmlspecialchars($pid)?>"
-      >
-      </div>
+		<div id="service-container"
+			class="service-container"
+			data-checklists="<?= htmlspecialchars(json_encode($clManager->getResearchPoints()))?>"
+			data-pid="<?= $pid ?>"></div>
 	</body>
 </html>
diff --git a/checklists/clsppeditor.php b/checklists/clsppeditor.php
@@ -10,7 +10,7 @@
 $tabIndex = array_key_exists('tabindex', $_POST) ? filter_var($_POST['tabindex'], FILTER_SANITIZE_NUMBER_INT) : 0;
 $action = array_key_exists('action', $_POST) ? htmlspecialchars($_POST['action'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) : '';
 $cltype = array_key_exists('cltype', $_POST) ? htmlspecialchars($_POST['cltype'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) : '';
-$renametid = array_key_exists('renametid', $_POST) ? htmlspecialchars($_POST['renametid'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) : '';
+$renametid = array_key_exists('renametid', $_POST) ? filter_var($_POST['renametid'], FILTER_SANITIZE_NUMBER_INT) : '';
 $locality = array_key_exists('locality', $_POST) ? htmlspecialchars($_POST['locality'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) : '';
 $habitat = array_key_exists('habitat', $_POST) ? htmlspecialchars($_POST['habitat'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) : '';
 $abundance = array_key_exists('abundance', $_POST) ? htmlspecialchars($_POST['abundance'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) : '';
@@ -101,6 +101,15 @@
 							$( "#renamesciname" ).val(ui.item.value);
 							$( "#renametid" ).val(ui.item.id);
 						}
+					},
+					change: function( event, ui ) {
+						if(ui.item === null) {
+							$( "#renametid" ).val("");
+							if($( "#renamesciname" ).val() != ""){
+								alert('<?= $LANG['SELECT_TAXON'] ?>');
+								f.renamesciname.focus();
+							}
+						}
 					}
 				});
 
@@ -111,32 +120,19 @@
 			});
 
 			function validateRenameForm(f){
-				if(f.renamesciname.value == ""){
+				if (f.renamesciname.value !== "" && f.renametid.value !== ""){
+					f.submit();
+				}
+				else if(f.renamesciname.value == ""){
 					alert("<?php echo $LANG['NAME_BLANK']; ?>");
 				}
-				else{
-					checkScinameExistence(f);
+				else {
+					alert('<?= $LANG['SELECT_TAXON'] ?>');
 				}
+				f.renamesciname.focus();
 				return false;
 			}
 
-			function checkScinameExistence(f){
-				$.ajax({
-					type: "POST",
-					url: "rpc/gettid.php",
-					data: { sciname: f.renamesciname.value }
-				}).done(function( renameTid ) {
-					if(renameTid){
-						if(f.renametid.value == "") f.renametid.value = renameTid;
-						f.submit();
-					}
-					else{
-						alert("<?php echo $LANG['SCINAME_ERROR']; ?>");
-						f.renametid.value = "";
-					}
-				});
-			}
-
 			function openPopup(urlStr,windowName){
 				newWindow = window.open(urlStr,windowName,'scrollbars=1,toolbar=0,resizable=1,width=800,height=650,left=20,top=20');
 				if (newWindow.opener == null) newWindow.opener = self;

diff --git a/checklists/index.php b/checklists/index.php
@@ -59,11 +59,20 @@
 					<h2 class="checklist-header">
 						<?php
 						$projName = $projArr['name'];
+						if($pid) echo '<a href="../projects/index.php?pid=' . $pid . '">';
 						if($projName == 'Miscellaneous Inventories') $projName = $LANG['MISC_INVENTORIES'];
 						echo $projName;
+						if($pid) echo '</a>';
+						if(!empty($projArr['displayMap'])){
+							?>
+							<a href="<?php echo "clgmap.php?pid=" . $pid; ?>" title='<?= $LANG['SHOW_MAP'] ?>'>
+								<img src='../images/world.png' style='width:10px;border:0' />
+							</a>
+							<?php
+						}
 						?>
-						<a class="button button-tertiary btn-medium-font" style="gap:0.5rem" href="<?php echo "clgmap.php?pid=" . htmlspecialchars($pid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE); ?>" title='<?php echo htmlspecialchars($LANG['SHOW_MAP'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE); ?>'>
-							<?php echo $LANG['MAP']; ?> <img src='../images/world.png' style='width:1em;border:0' alt='<?php echo $LANG['IMG_OF_GLOBE']; ?>' />
+						<a class="button button-tertiary btn-medium-font" style="gap:0.5rem" href="<?= "clgmap.php?pid=" . $pid ?>" title='<?= $LANG['SHOW_MAP'] ?>'>
+							<?= $LANG['MAP'] ?> <img src='../images/world.png' style='width:1em;border:0' alt='<?= $LANG['IMG_OF_GLOBE'] ?>' />
 						</a>
 					</h2>
 					<ul class="checklist-ul">

diff --git a/checklists/rpc/gettid.php b/checklists/rpc/gettid.php
diff --git a/checklists/tools/mappointaid.php b/checklists/tools/mappointaid.php
@@ -1,16 +1,16 @@
 <?php
 include_once('../../config/symbini.php');
-include_once($SERVER_ROOT.'/content/lang/collections/tools/mapaids.'.$LANG_TAG.'.php');
-header("Content-Type: text/html; charset=".$CHARSET);
-if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT.'/content/lang/header.' . $LANG_TAG . '.php')) include_once($SERVER_ROOT . '/content/lang/header.en.php');
-else include_once($SERVER_ROOT . '/content/lang/header.' . $LANG_TAG . '.php');
-
-$formName = array_key_exists("formname",$_REQUEST)?$_REQUEST["formname"]:"";
-$latName = array_key_exists("latname",$_REQUEST)?$_REQUEST["latname"]:"";
-$longName = array_key_exists("longname",$_REQUEST)?$_REQUEST["longname"]:"";
-$latDef = array_key_exists("latdef",$_REQUEST)?$_REQUEST["latdef"]:0;
-$lngDef = array_key_exists("lngdef",$_REQUEST)?$_REQUEST["lngdef"]:0;
-$zoom = array_key_exists("zoom",$_REQUEST)&&$_REQUEST["zoom"]?$_REQUEST["zoom"]:5;
+header('Content-Type: text/html; charset=' . $CHARSET);
+if($LANG_TAG == 'en' || !file_exists($SERVER_ROOT.'/content/lang/collections/tools/mapaids.' . $LANG_TAG . '.php')) include_once($SERVER_ROOT . '/content/lang/collections/tools/mapaids.en.php');
+else include_once($SERVER_ROOT . '/content/lang/collections/tools/mapaids.' . $LANG_TAG . '.php');
+
+$formName = array_key_exists('formname', $_REQUEST) ? htmlspecialchars($_REQUEST['formname'], HTML_SPECIAL_CHARS_FLAGS) : '';
+$latName = array_key_exists('latname', $_REQUEST) ? htmlspecialchars($_REQUEST['latname'], HTML_SPECIAL_CHARS_FLAGS) : '';
+$longName = array_key_exists('longname', $_REQUEST) ? htmlspecialchars($_REQUEST['longname'], HTML_SPECIAL_CHARS_FLAGS) : '';
+$latDef = array_key_exists('latdef', $_REQUEST) ? filter_var($_REQUEST['latdef'], FILTER_SANITIZE_NUMBER_FLOAT) : 0;
+$lngDef = array_key_exists('lngdef', $_REQUEST) ? filter_var($_REQUEST['lngdef'], FILTER_SANITIZE_NUMBER_FLOAT) : 0;
+$zoom = !empty($_REQUEST['zoom']) ? filter_var($_REQUEST['zoom'], FILTER_SANITIZE_NUMBER_INT) : 5;
+
 if($latDef == 0 && $lngDef == 0){
 	$latDef = '';
 	$lngDef = '';

diff --git a/classes/ChecklistManager.php b/classes/ChecklistManager.php
@@ -685,17 +685,22 @@ public function addNewSpecies($postArr){
 	//Checklist index page functions
 	public function getChecklists($limitToKey=false){
 		$retArr = Array();
-		$sql = 'SELECT p.pid, p.projname, p.ispublic, c.clid, c.name, c.access, c.defaultSettings, COUNT(l.tid) AS sppcnt
+		$sql = 'SELECT p.pid, p.projname, p.ispublic, c.clid, c.name, c.access, c.defaultSettings, c.latCentroid
 			FROM fmchecklists c LEFT JOIN fmchklstprojlink cpl ON c.clid = cpl.clid
-			INNER JOIN fmchklsttaxalink l ON c.clid = l.clid
 			LEFT JOIN fmprojects p ON cpl.pid = p.pid
-			WHERE ((c.access LIKE "public%") ';
-		if(isset($GLOBALS['USER_RIGHTS']['ClAdmin']) && $GLOBALS['USER_RIGHTS']['ClAdmin']) $sql .= 'OR (c.clid IN('.implode(',',$GLOBALS['USER_RIGHTS']['ClAdmin']).'))';
+			WHERE c.type != "excludespp" AND ((c.access LIKE "public%") ';
+		if(isset($GLOBALS['USER_RIGHTS']['ClAdmin']) && $GLOBALS['USER_RIGHTS']['ClAdmin']){
+			$sql .= 'OR (c.clid IN('.implode(',',$GLOBALS['USER_RIGHTS']['ClAdmin']).'))';
+		}
 		$sql .= ') AND ((p.pid IS NULL) OR (p.ispublic = 1) ';
-		if(isset($GLOBALS['USER_RIGHTS']['ProjAdmin']) && $GLOBALS['USER_RIGHTS']['ProjAdmin']) $sql .= 'OR (p.pid IN('.implode(',',$GLOBALS['USER_RIGHTS']['ProjAdmin']).'))';
+		if(isset($GLOBALS['USER_RIGHTS']['ProjAdmin']) && $GLOBALS['USER_RIGHTS']['ProjAdmin']){
+			$sql .= 'OR (p.pid IN('.implode(',',$GLOBALS['USER_RIGHTS']['ProjAdmin']).'))';
+		}
 		$sql .= ') ';
 		if($this->pid) $sql .= 'AND (p.pid = '.$this->pid.') ';
-		$sql .= 'GROUP BY p.projname, c.Name HAVING sppcnt > 10';
+		//Following line limits result to only checklists that have a linked taxon or is a parent checklist with possible inherited taxa
+		$sql .= 'AND c.clid IN(SELECT clid FROM fmchklsttaxalink UNION DISTINCT SELECT clid FROM fmchklstchildren) ';
+		$sql .= 'ORDER BY p.projname, c.name';
 		$rs = $this->conn->query($sql);
 		while($row = $rs->fetch_object()){
 			if($limitToKey){
@@ -709,6 +714,7 @@ public function getChecklists($limitToKey=false){
 				$pid = 0;
 				$projName = 'Miscellaneous Inventories';
 			}
+			if($row->latCentroid) $retArr[$pid]['displayMap'] = 1;
 			$retArr[$pid]['name'] = $this->cleanOutStr($projName);
 			$retArr[$pid]['clid'][$row->clid] = $this->cleanOutStr($row->name).($row->access=='private'?' (Private)':'');
 		}
@@ -774,11 +780,14 @@ public function getSpeciesSearch($term){
 		$term = preg_replace('/[^a-zA-Z\-\. ]+/', '', $term);
 		$term = preg_replace('/\s{1}x{1}\s{0,1}$/i', ' _ ', $term);
 		$term = preg_replace('/\s{1}[\D]{1}\s{1}/i', ' _ ', $term);
+
 		if($term){
+
 			$sql = 'SELECT tid, sciname, author FROM taxa WHERE (rankid > 179) AND (sciname LIKE "'.$term.'%")';
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
-				$retArr[] = $r->sciname . ' ' . $r->author;
+				$retArr[] = (object) [ 'value' => $r->sciname . ' ' . $r->author,
+				'id' => $r->tid];
 			}
 			$rs->free();
 		}

diff --git a/classes/DwcArchiverPublisher.php b/classes/DwcArchiverPublisher.php
@@ -316,22 +316,27 @@ private function aasort(&$array, $key){
 	}
 
 	public function humanFileSize($filePath) {
+		$x = false;
 		if(substr($filePath,0,4)=='http') {
-			$x = array_change_key_case(get_headers($filePath, 1),CASE_LOWER);
-			if( strcasecmp($x[0], 'HTTP/1.1 200 OK') != 0 ) {
-				$x = $x['content-length'][1];
-			}
-			else {
-				$x = $x['content-length'];
+			if($headerArr = @get_headers($filePath, 1)){
+				$x = array_change_key_case($headerArr, CASE_LOWER);
+				if( strcasecmp($x[0], 'HTTP/1.1 200 OK') != 0 ) {
+					$x = $x['content-length'][1];
+				}
+				else {
+					$x = $x['content-length'];
+				}
 			}
 		}
 		else {
 			$x = @filesize($filePath);
 		}
-		$x = round($x/1000000, 1);
-		if(!$x) $x = 0.1;
-
-		return $x.'M ';
+		if($x !== false){
+			$x = round($x/1000000, 1);
+			if(!$x) $x = 0.1;
+			return $x.'M';
+		}
+		return '?M';
 	}
 }
 ?>
diff --git a/classes/OccurrenceIndividual.php b/classes/OccurrenceIndividual.php
@@ -259,7 +259,7 @@ private function setDeterminations(){
 
 	private function setImages(){
 	    global $IMAGE_DOMAIN;
-		$sql = 'SELECT i.imgid, i.url, i.thumbnailurl, i.originalurl, i.sourceurl, i.notes, i.caption, 
+		$sql = 'SELECT i.imgid, i.url, i.thumbnailurl, i.originalurl, i.sourceurl, i.notes, i.caption,
             CONCAT_WS(" ",u.firstname,u.lastname) as innerPhotographer, i.photographer, i.rights, i.accessRights, i.copyright
 			FROM images i LEFT JOIN users u ON i.photographeruid = u.uid
 			WHERE (i.occid = ?) ORDER BY i.sortoccurrence,i.sortsequence';
@@ -275,7 +275,7 @@ private function setImages(){
 					if($IMAGE_DOMAIN){
 					    if(substr($url,0,1)=='/') $url = $IMAGE_DOMAIN . $url;
 					    if($lgUrl && substr($lgUrl, 0, 1) == '/') $lgUrl = $IMAGE_DOMAIN . $lgUrl;
-						if($tnUrl && substr($tnUrl, 0, 1) == '/') $tnUrl = $imageDomain . $tnUrl;
+					    if($tnUrl && substr($tnUrl, 0, 1) == '/') $tnUrl = $IMAGE_DOMAIN . $tnUrl;
 					}
 					if((!$url || $url == 'empty') && $lgUrl) $url = $lgUrl;
 					if(!$tnUrl && $url) $tnUrl = $url;

diff --git a/classes/OccurrenceMapManager.php b/classes/OccurrenceMapManager.php
@@ -347,7 +347,7 @@ public function writeKMLFile($recLimit, $extraFieldArr = null){
 		$cnt = 0;
 		$coordArr = $this->getMappingData($recLimit, $extraFieldArr);
 		if($coordArr){
-			$this->googleIconArr = array('pushpin/ylw-pushpin','pushpin/blue-pushpin','pushpin/grn-pushpin','pushpin/ltblu-pushpin',
+			$googleIconArr = array('pushpin/ylw-pushpin','pushpin/blue-pushpin','pushpin/grn-pushpin','pushpin/ltblu-pushpin',
 				'pushpin/pink-pushpin','pushpin/purple-pushpin', 'pushpin/red-pushpin','pushpin/wht-pushpin','paddle/blu-blank',
 				'paddle/grn-blank','paddle/ltblu-blank','paddle/pink-blank','paddle/wht-blank','paddle/blu-diamond','paddle/grn-diamond',
 				'paddle/ltblu-diamond','paddle/pink-diamond','paddle/ylw-diamond','paddle/wht-diamond','paddle/red-diamond','paddle/purple-diamond',
@@ -359,7 +359,7 @@ public function writeKMLFile($recLimit, $extraFieldArr = null){
 			foreach($coordArr as $sciname => $snArr){
 				unset($snArr['tid']);
 				$cnt++;
-				$iconStr = $this->googleIconArr[$cnt%44];
+				$iconStr = $googleIconArr[$cnt%44];
 				echo "<Style id='sn_".$iconStr."'>\n";
 				echo "<IconStyle><scale>1.1</scale><Icon>";
 				echo "<href>http://maps.google.com/mapfiles/kml/" . htmlspecialchars($iconStr, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . ".png</href>";