Merge branch 'Development' into change-innertext-width-search-index

BioKIC · May 15, 2024 · 90fb6f0 · 90fb6f0
2 parents d00f8ed + 065ae1e
commit 90fb6f0
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Showing 296 changed files with 880 additions and 630 deletions.
diff --git a/admin/index.php b/admin/index.php
@@ -17,7 +17,7 @@
 		$displayLeftMenu = true;
 		include($SERVER_ROOT.'/includes/header.php');
 		?>
-		<div id="innertext">
+		<div role="main" id="innertext">
 			<h1><?php echo $LANG['FORBIDDEN']; ?></h1>
 			<div style="font-weight:bold;">
 				<?php echo $LANG['NO_PERMISSION']; ?>

diff --git a/admin/portalindex.php b/admin/portalindex.php
@@ -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';

diff --git a/admin/schemamanager.php b/admin/schemamanager.php
@@ -37,7 +37,7 @@
 		<?php
 		include($SERVER_ROOT.'/includes/header.php');
 		?>
-		<div id="innertext">
+		<div role="main" id="innertext">
 			<h1>Database Schema Manager</h1>
 			<?php
 			if($IS_ADMIN || !$curentVersion){

diff --git a/agents/rpc/index.php b/agents/rpc/index.php
@@ -17,7 +17,7 @@
 		include($SERVER_ROOT.'/includes/header.php');
 		?>
 		<!-- This is inner text! -->
-		<div id="innertext">
+		<div role="main" id="innertext">
 			<h1 class="page-heading">Forbidden</h1>
 			<div style="font-weight:bold;">
 				You don't have permission to access this page.

diff --git a/checklists/checklist.php b/checklists/checklist.php
@@ -142,6 +142,7 @@ function changeImageSource(elem){
 		}
 		?>
 		#editsppon { display: none; color:green; font-size: 70%; font-weight:bold; padding-bottom: 5px; position: relative; top: -4px; }
+		.moredetails{ clear: both }
 		.normal-font-weight {
 			font-weight: normal;
 		}
@@ -584,7 +585,7 @@ function changeImageSource(elem){
 							?>
 						</div>
 					</div>
-					<hr />
+					<hr style="margin-right: 2rem"/>
 					<div class="printoff">
 						<?php
 						$taxaLimit = ($showImages?$clManager->getImageLimit():$clManager->getTaxaLimit());
@@ -610,7 +611,7 @@ function changeImageSource(elem){
 						}
 						?>
 					</div>
-					<hr />
+					<hr style="margin-right: 2rem"/>
 					<?php
 					if($showImages){
 						$prevfam = '';

diff --git a/checklists/checklistadmin.php b/checklists/checklistadmin.php
@@ -326,7 +326,7 @@ function validateAddProjectForm(f){
 					<div style="margin:15px;">
 						<form name="deleteclform" action="checklistadmin.php" method="post" onsubmit="return window.confirm('<?php echo $LANG['CONFIRMDELETE'];?>')">
 							<input name="delclid" type="hidden" value="<?php echo $clid; ?>" />
-							<button name="submitaction" type="submit" value="deleteChecklist"  aria-label="<?php echo $LANG['DELETECHECK'];?>" <?php if($projArr || count($editorArr) > 1) echo 'DISABLED'; ?>><?php echo $LANG['DELETECHECK'];?></button>
+							<button class="button-danger" name="submitaction" type="submit" value="deleteChecklist"  aria-label="<?php echo $LANG['DELETECHECK'];?>" <?php if($projArr || count($editorArr) > 1) echo 'DISABLED'; ?>><?php echo $LANG['DELETECHECK'];?></button>
 						</form>
 					</div>
 				</div>
@@ -392,4 +392,4 @@ function validateAddProjectForm(f){
 include($SERVER_ROOT.'/includes/footer.php');
 ?>
 </body>
-</html>
+</html>
diff --git a/checklists/checklistadminchildren.php b/checklists/checklistadminchildren.php
@@ -60,7 +60,7 @@ function validateAddChildForm(f){
 	button{ margin:20px; }
 </style>
 <!-- inner text -->
-<div id="innertext" style="background-color:white;">
+<div role="main" id="innertext" style="background-color:white;">
 	<div style="float:right;">
 		<a href="#" onclick="toggle('addchilddiv')"><img src="../images/add.png" style="width:1.5em;" /></a>
 	</div>

diff --git a/checklists/checklistadminmeta.php b/checklists/checklistadminmeta.php
@@ -262,7 +262,7 @@ function enableDisableExtServiceFields() {
 						<?php echo $LANG['POLYGON_NOT_DEFINED']; ?>
 					</span>
 					<span style="margin:10px;"><a href="#" onclick="openMappingPolyAid();return false;" title="<?php echo $LANG['CREATE_EDIT_POLYGON']; ?>"><img src="../images/world.png" style="width:1em;" /></a></span>
-					<input type="hidden" id="footprintwkt" name="footprintwkt" value="" />
+					<input type="hidden" id="footprintwkt" name="footprintwkt" value="<?= $clArray['footprintwkt']?>" />
 				</fieldset>
 			</div>
 			<div style="clear:both;margin-top:5px;">
@@ -318,7 +318,7 @@ function enableDisableExtServiceFields() {
 						<?php
 						// Activate Identification key: 0 = false, 1 = true
 						$activateKey = $KEY_MOD_IS_ACTIVE;
-						if(array_key_exists('activatekey', $defaultArr)) $activateKey = $defaultArr["activatekey"];
+						if(array_key_exists('activatekey', $defaultArr??[])) $activateKey = $defaultArr["activatekey"];
 						?>
 						<input name='activatekey' type='checkbox' value='1' <?php echo ($activateKey?"checked":""); ?> />
 						<?php echo $LANG['ACTIVATEKEY']; ?>
@@ -420,4 +420,4 @@ function enableDisableExtServiceFields() {
 		}
 	}
 	?>
-</div>
+</div>
diff --git a/checklists/clsppeditor.php b/checklists/clsppeditor.php
@@ -274,7 +274,7 @@ function removeTaxon(){
 								<input type="hidden" name='clid' value="<?php echo $vManager->getClid(); ?>" />
 								<input type="hidden" name='cltype' value="<?php echo $clArray['cltype']; ?>" />
 								<input type="hidden" name='locality' value="<?php echo $clArray['locality']; ?>" />
-								<button type="submit" name="action" value="deleteTaxon"><?php echo $LANG['DELETE_TAXON']; ?></button>
+								<button class="button-danger" type="submit" name="action" value="deleteTaxon"><?php echo $LANG['DELETE_TAXON']; ?></button>
 							</fieldset>
 						</form>
 					</div>
@@ -363,4 +363,4 @@ function removeTaxon(){
 			?>
 		</div>
 	</body>
-</html>
+</html>
diff --git a/checklists/imgvouchertab.php b/checklists/imgvouchertab.php
@@ -31,8 +31,10 @@
 				<input type="hidden" name="clid" value="<?php echo $clid; ?>" />
 			</div>
 			<div style="margin:5px;">
-				<input type="submit" name="submitvoucher" value=<?php echo $LANG['ADDIMGVOUC'];?> /><br/>
+				<button type="submit" name="submitvoucher">
+					<?php echo $LANG['ADDIMGVOUC'];?>
+				</button>
 			</div>
 		</fieldset>
 	</form>
-</div>
+</div>
diff --git a/checklists/index.php b/checklists/index.php
@@ -39,7 +39,7 @@
 		<a href="../index.php"><?php echo htmlspecialchars($LANG['NAV_HOME'], ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE); ?></a> &gt;&gt;
 		<b><?php echo $LANG['SPECIES_INVENTORIES']; ?></b>
 	</div>
-	<div id="innertext">
+	<div role="main" id="innertext">
 		<h1 class="page-heading"><?= $LANG['SPECIES_INVENTORIES']; ?></h1>
         <div style="margin:20px;">
 			<?php

diff --git a/checklists/rpc/index.php b/checklists/rpc/index.php
@@ -20,7 +20,7 @@
 		include($SERVER_ROOT.'/includes/header.php');
 		?>
 		<!-- This is inner text! -->
-		<div id="innertext">
+		<div role="main" id="innertext">
 			<h1> <?php echo $LANG['FORBIDDEN']; ?> </h1>
 			<div style="font-weight:bold;">
 				<?php echo $LANG['NO_PERMISSION']; ?>

diff --git a/checklists/tools/checklistloader.php b/checklists/tools/checklistloader.php
@@ -64,7 +64,7 @@ function displayErrors(clickObj){
 		<a href="checklistloader.php?clid=<?php echo htmlspecialchars($clid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '&pid=' . htmlspecialchars($pid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE); ?>"><b><?php echo $LANG['CHECK_LOADER']; ?></b></a>
 	</div>
 	<!-- This is inner text! -->
-	<div id="innertext">
+	<div role="main" id="innertext">
 		<h1>
 			<a href="<?php echo $CLIENT_ROOT."/checklists/checklist.php?clid=" . htmlspecialchars($clid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE) . '&pid=' . htmlspecialchars($pid, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE); ?>">
 				<?php echo $clMeta['name']; ?>

diff --git a/checklists/tools/index.php b/checklists/tools/index.php
@@ -17,7 +17,7 @@
 		include($SERVER_ROOT.'/includes/header.php');
 		?>
 		<!-- This is inner text! -->
-		<div id="innertext">
+		<div role="main" id="innertext">
 			<h1 class="page-heading">Checklist Tools</h1>
 			<h1 class="page-heading">Forbidden</h1>
 			<div style="font-weight:bold;">

diff --git a/checklists/tools/mappolyaid.php b/checklists/tools/mappolyaid.php
@@ -71,6 +71,10 @@
          //Default is that trim is checked and lnglat/switchCoord is not
          let trimPolyFlag = true;
          let lnglatLayoutFlag = false;
+		 let action = "<?= htmlspecialchars($formSubmit) ?>"
+		 if(action === 'exit') {
+			 window.close();
+		 }
 
          function onPolyUpdate(shape) {
             setWkt(map.shapes);
@@ -215,8 +219,11 @@ function initialize() {
             let polygons;
 
             //Loads wkt from opener value otherwise db value is used
-            let wkt = opener.document.getElementById("footprintwkt").value;
-            if(wkt) document.getElementById("footprintwkt").value = wkt;
+            let parent_wkt = opener.document.getElementById("footprintwkt");
+			 console.log(parent_wkt)
+			if(parent_wkt) {
+				document.getElementById("footprintwkt").value = parent_wkt.value 
+			}
 
             if(<?= (!empty($GOOGLE_MAP_KEY)?'true':'false') ?>) {
                googleInit();
@@ -262,8 +269,11 @@ function submitPolygonForm(f){
 					opener.document.getElementById("polyDefDiv").style.display = str1;
 					opener.document.getElementById("polyNotDefDiv").style.display = str2;
 				}
-            opener.document.getElementById("footprintwkt").value = f.footprintwkt.value;
-				window.close();
+				if(opener.document.getElementById("footprintwkt")) {
+					opener.document.getElementById("footprintwkt").value = f.footprintwkt.value;
+					// If Tool is filling out form value from parent form don't finish action on itself just forward value to parent form
+					window.close();
+				}
 				return f.clid.value != 0;
 			}
 		</script>

diff --git a/checklists/vaconflicts.php b/checklists/vaconflicts.php
@@ -43,7 +43,7 @@ function validateBatchConflictForm(f){
 		f.submit();
 	}
 </script>
-<div id="innertext" style="background-color:white;">
+<div role="main" id="innertext" style="background-color:white;">
 	<div style="margin-bottom:10px;">
 		<?php
 		echo $LANG['EXPLAIN_PARAGRAPH'];

diff --git a/checklists/vamissingtaxa.php b/checklists/vamissingtaxa.php
@@ -24,7 +24,7 @@
 	elseif($displayMode==2) $missingArr = $vManager->getMissingProblemTaxa();
 	else $missingArr = $vManager->getMissingTaxa();
 	?>
-	<div id="innertext" style="background-color:white;">
+	<div role="main" id="innertext" style="background-color:white;">
 		<div style='float:left;font-weight:bold;margin-left:5px'>
 			<?php
 			if($displayMode == 2){

diff --git a/checklists/voucheradmin.php b/checklists/voucheradmin.php
@@ -198,7 +198,7 @@
 									<b><?php echo $LANG['LATN'];?>:</b>
 									<input id="upperlat" type="text" name="latnorth" style="width:80px;" value="<?php echo isset($termArr['latnorth'])?$termArr['latnorth']:''; ?>" title="<?php echo $LANG['LAT_NORTH'] ?>" />
 									<?php
-									$coordAidUrl = '../collections/tools/mapcoordaid.php?mapmode=rectangle&latdef='.$clMetaArr['latcentroid'].'&lngdef='.$clMetaArr['longcentroid'];
+									$coordAidUrl = '../collections/tools/mapcoordaid.php?map_mode_strict=true&mapmode=rectangle&latdef='.$clMetaArr['latcentroid'].'&lngdef='.$clMetaArr['longcentroid'];
 									?>
 									<a href="#" onclick="openPopup('<?php echo htmlspecialchars($coordAidUrl, ENT_COMPAT | ENT_HTML401 | ENT_SUBSTITUTE); ?>','boundingbox')"><img src="../images/world.png" style="width:1.2em" title="<?php echo $LANG['FIND_COORD'] ?>" /></a>
 								</div>
@@ -233,7 +233,9 @@
 					<tr>
 						<td colspan="2">
 							<div style="margin:10px;">
-								<input type="submit" name="submit" value="<?php echo $LANG['SAVESEARCH'];?>" />
+								<button type="submit">
+									<?php echo $LANG['SAVESEARCH'];?>
+								</button>
 								<input type="hidden" name="submitaction" value="SaveSearch" />
 								<input type='hidden' name='clid' value='<?php echo $clid; ?>' />
 								<input type='hidden' name='pid' value='<?php echo $pid; ?>' />
@@ -250,8 +252,10 @@
 				<legend><b><?php echo $LANG['REMOVESEARCH'];?></b></legend>
 				<form name="sqldeleteform" action="voucheradmin.php" method="post" onsubmit="return confirm('<?php echo $LANG['SURE_DELETE_QUERY'];?>');">
 					<div style="margin:20px">
-						<input type="submit" name="submit" value="<?php echo $LANG['DELETEVARIABLES'];?>" />
-						<input type="hidden" name="submitaction" value="DeleteVariables" />
+					<button class="button-danger" type="submit">
+						<?php echo $LANG['DELETEVARIABLES'];?>
+					</button>
+					<input type="hidden" name="submitaction" value="DeleteVariables" />
 					</div>
 					<input type="hidden" name="clid" value="<?php echo $clid; ?>" />
 					<input type="hidden" name="pid" value="<?php echo $pid; ?>" />
@@ -322,4 +326,4 @@
 include($SERVER_ROOT.'/includes/footer.php');
 ?>
 </body>
-</html>
+</html>
diff --git a/classes/ChecklistAdmin.php b/classes/ChecklistAdmin.php
@@ -39,8 +39,8 @@ public function createChecklist($postArr){
 				//Add permissions to allow creater to be an editor and then reset user permissions stored in browser cache
 				$inventoryManager->insertUserRole($GLOBALS['SYMB_UID'], 'ClAdmin', 'fmchecklists', $newClid, $GLOBALS['SYMB_UID']);
 				$newPManager = new ProfileManager();
-				$newPManager->setUserName($GLOBALS['USERNAME']);
-				$newPManager->authenticate();
+				$newPManager->setUid($GLOBALS['SYMB_UID']);
+				$newPManager->setUserRights();
 				if($postArr['type'] == 'excludespp' && $postArr['excludeparent']){
 					//If is an exclusion checklists, link to parent checklist
 					if(!$inventoryManager->insertChildChecklist($postArr['excludeparent'], $newClid, $GLOBALS['SYMB_UID'])){
@@ -615,7 +615,7 @@ public function getClName(){
 
 	//Misc support functions
 	public function cleanOutArray($inputArray){
-		$skip = array('defaultsettings', 'dynamicsql', 'footprintWkt');
+		$skip = array('defaultsettings', 'dynamicsql', 'footprintwkt');
 		if(is_array($inputArray)){
 			foreach($inputArray as $key => $value){
 				if(is_array($value)){
@@ -631,4 +631,4 @@ public function cleanOutArray($inputArray){
 		return $inputArray;
 	}
 }
-?>
+?>
diff --git a/classes/DwcArchiverBaseManager.php b/classes/DwcArchiverBaseManager.php
@@ -42,6 +42,7 @@ public function writeOutRecordBlock($occidArr){
 					$this->writeOutRecord($r);
 				}
 				$rs->free();
+				fclose($this->fileHandler);
 			}
 			else{
 				$this->logOrEcho('ERROR writing out to extension file: '.$this->conn->error."\n");

diff --git a/classes/DwcArchiverCore.php b/classes/DwcArchiverCore.php
@@ -1790,11 +1790,11 @@ private function writeOccurrenceFile(){
 			}
 			if ($this->includeAttributes){
 				$this->writeAttributeData($batchOccidArr);
-				if($this->attributeHandler !== null) $this->attributeHandler->__destruct();
+				if($this->attributeHandler !== null) $this->attributeHandler = null;
 			}
 			if ($this->includeMaterialSample){
 				$this->writeMaterialSampleData($batchOccidArr);
-				if($this->materialSampleHandler !== null) $this->materialSampleHandler->__destruct();
+				if($this->materialSampleHandler !== null) $this->materialSampleHandler = null;
 			}
 		}
 		else {

diff --git a/classes/ImInventories.php b/classes/ImInventories.php
@@ -44,6 +44,7 @@ public function getChecklistMetadata($pid = null){
 				$retArr['defaultsettings'] = $row->defaultsettings;
 				$retArr['dynamicsql'] = $row->dynamicsql;
 				$retArr['hasfootprintwkt'] = ($row->footprintwkt?'1':'0');
+				$retArr['footprintwkt'] = $row->footprintwkt;
 				$retArr['sortsequence'] = $row->sortsequence;
 				$retArr['datelastmodified'] = $row->datelastmodified;
 				$retArr['dynamicProperties'] = $row->dynamicProperties;
@@ -695,4 +696,4 @@ public function getPrimaryKey(){
 		return $this->primaryKey;
 	}
 }
-?>
+?>
diff --git a/classes/ImageLibrarySearch.php b/classes/ImageLibrarySearch.php
@@ -363,7 +363,7 @@ public function getDbStr(){
 	}
 
 	public function setCollectionVariables($reqArr){
-		$this->dbStr = trim(OccurrenceSearchSupport::getDbRequestVariable(), '; ');
+		$this->dbStr = trim(OccurrenceSearchSupport::getDbRequestVariable(), ',; ');
 	}
 
 	public function setTaxonType($t){
@@ -448,4 +448,4 @@ public function getErrorStr(){
 		return $this->errorStr;
 	}
 }
-?>
+?>
diff --git a/classes/OccurrenceMapManager.php b/classes/OccurrenceMapManager.php
@@ -478,7 +478,7 @@ public function getObservationIds(){
 
 	//Misc support functions
 	private function htmlEntities($string){
-		return htmlspecialchars($string, ENT_XML1 | ENT_QUOTES, 'UTF-8');
+		return htmlspecialchars($string ?? '', ENT_XML1 | ENT_QUOTES, 'UTF-8');
 	}
 }
 ?>
diff --git a/classes/OccurrenceSearchSupport.php b/classes/OccurrenceSearchSupport.php
@@ -368,16 +368,10 @@ public static function getDbWhereFrag($dbSearchTerm){
 			}
 			elseif($dbSearchTerm == 'allobs'){
 				$sqlRet .= 'AND (o.collid IN(SELECT collid FROM omcollections WHERE colltype IN("General Observations","Observations"))) ';
-			}
-			else{
+			} else {
+				// Check in case there is ; inside dbSearchTerm
 				$dbArr = explode(';',$dbSearchTerm);
-				$dbStr = '';
-				if(isset($dbArr[0]) && $dbArr[0]){
-					$dbStr = "(o.collid IN(".$dbArr[0].")) ";
-				}
-				if(isset($dbArr[1]) && $dbArr[1]){
-					//$dbStr .= ($dbStr?'OR ':'').'(o.CollID IN(SELECT collid FROM omcollcatlink WHERE (ccpk IN('.$dbArr[1].')))) ';
-				}
+				$dbStr = "o.collid IN(" . (is_array($dbArr)? implode(',', $dbArr): $dbArr) . ")";
 				$sqlRet .= 'AND ('.$dbStr.') ';
 			}
 		}

diff --git a/classes/ProfileManager.php b/classes/ProfileManager.php
@@ -478,7 +478,7 @@ public function loginExists($login){
 		return $status;
 	}
 
-	protected function setUserRights(){
+	public function setUserRights(){
 		if($this->uid){
 			$userRights = array();
 			$sql = 'SELECT role, tablepk FROM userroles WHERE (uid = ?) ';