Merge pull request egbot#308 from BioKIC/master

Merge BioKIC/Symbiota developments

checklists/checklistadmin.php

@@ -14,26 +14,23 @@
 if(!$clid && isset($_POST['delclid'])) $clid = $_POST['delclid'];
 $clManager->setClid($clid);
 
-
 $statusStr = '';
-if($action == 'SubmitAdd'){
-
-	//Conform User Checklist permission 
-	if($IS_ADMIN || (array_key_exists('ClAdmin',$USER_RIGHTS) && in_array($clid,$USER_RIGHTS['ClAdmin'])) || array_key_exists('ClCreate',$USER_RIGHTS)){		
+if($action == 'submitAdd'){
+	//Conform User Checklist permission
+	if($IS_ADMIN || (array_key_exists('ClAdmin',$USER_RIGHTS) && in_array($clid,$USER_RIGHTS['ClAdmin'])) || array_key_exists('ClCreate',$USER_RIGHTS)){
 		$newClid = $clManager->createChecklist($_POST);
-		header('Location: checklist.php?clid='.$newClid);
-	} 
-
+		if($newClid) header('Location: checklist.php?clid='.$newClid);
+	}
 	//If we made it here the user does not have any checklist roles. cancel further execution.
-	$statusStr = 'You do not have permission to create a Checklist.';
+	$statusStr = 'You do not have permission to create a Checklist. Please contact an administrator.';
 }
 
 $isEditor = 0;
 if($IS_ADMIN || (array_key_exists('ClAdmin',$USER_RIGHTS) && in_array($clid,$USER_RIGHTS['ClAdmin']))){
 	$isEditor = 1;
 
 	//Submit checklist MetaData edits
-	if($action == 'SubmitEdit'){
+	if($action == 'submitEdit'){
 		$clManager->editMetaData($_POST);
 		header('Location: checklist.php?clid='.$clid.'&pid='.$pid);
 	}

checklists/checklistadminmeta.php

@@ -306,16 +306,10 @@ function openMappingPolyAid() {
 			<div style="clear:both;float:left;margin-top:15px;">
 				<?php
 				if($clid){
-					?>
-					<input type='submit' name='submit' value='<?php echo (isset($LANG['EDITCHECKLIST'])?$LANG['EDITCHECKLIST']:'Edit Checklist');?>' />
-					<input type="hidden" name="submitaction" value="SubmitEdit" />
-					<?php
+					echo '<button type="submit" name="submitaction" value="submitEdit">'.(isset($LANG['EDITCHECKLIST'])?$LANG['EDITCHECKLIST']:'Edit Checklist').'</button>';
 				}
 				else{
-					?>
-					<input type='submit' name='submit' value='<?php echo (isset($LANG['ADDCHECKLIST'])?$LANG['ADDCHECKLIST']:'Add Checklist');?>' />
-					<input type="hidden" name="submitaction" value="SubmitAdd" />
-					<?php
+					echo '<button type="submit" name="submitaction" value="submitAdd">'.(isset($LANG['ADDCHECKLIST'])?$LANG['ADDCHECKLIST']:'Add Checklist').'</button>';
 				}
 				?>
 			</div>

classes/DwcArchiverDetermination.php

@@ -2,6 +2,7 @@
 class DwcArchiverDetermination{
 
 	public static function getDeterminationArr($schemaType,$extended){
+		$fieldArr = array();
 		$fieldArr['coreid'] = 'o.occid';
 		$termArr['identifiedBy'] = 'http://rs.tdwg.org/dwc/terms/identifiedBy';
 		$fieldArr['identifiedBy'] = 'd.identifiedBy';
@@ -65,45 +66,21 @@ private static function trimBySchemaType($detArr,$schemaType,$extended){
 		return array_diff_key($detArr,array_flip($trimArr));
 	}
 
-	public static function getSqlDeterminations($fieldArr,$conditionSql){
+	public static function getSql($fieldArr, $tableJoins, $conditionSql){
 		$sql = '';
 		if($fieldArr && $conditionSql){
-			$sqlFrag = '';
-			foreach($fieldArr as $fieldName => $colName){
-				if($colName) $sqlFrag .= ', '.$colName;
+			$sql = 'SELECT ';
+			$delimiter = '';
+			foreach($fieldArr as $fieldSql){
+				if($fieldSql) $sql .= $delimiter.$fieldSql;
+				$delimiter = ', ';
 			}
-			$sql = 'SELECT '.trim($sqlFrag,', ').
-				' FROM omoccurdeterminations d INNER JOIN omoccurrences o ON d.occid = o.occid '.
-				'INNER JOIN guidoccurdeterminations g ON d.detid = g.detid '.
-				'LEFT JOIN taxa t ON d.tidinterpreted = t.tid ';
-			if(strpos($conditionSql,'ts.taxauthid')){
-				$sql .= 'LEFT JOIN taxstatus ts ON o.tidinterpreted = ts.tid ';
-			}
-			if(stripos($conditionSql,'e.parenttid')){
-				$sql .= 'LEFT JOIN taxaenumtree e ON o.tidinterpreted = e.tid ';
-			}
-			if(strpos($conditionSql,'v.clid')){
-				//Search criteria came from custom search page
-				$sql .= 'LEFT JOIN fmvouchers v ON o.occid = v.occid ';
-			}
-			if(strpos($conditionSql,'p.point')){
-				//Search criteria came from map search page
-				$sql .= 'LEFT JOIN omoccurpoints p ON o.occid = p.occid ';
-			}
-			if(strpos($conditionSql,'MATCH(f.recordedby)') || strpos($conditionSql,'MATCH(f.locality)')){
-				$sql .= 'INNER JOIN omoccurrencesfulltext f ON o.occid = f.occid ';
-			}
-			if(stripos($conditionSql,'a.stateid')){
-				//Search is limited by occurrence attribute
-				$sql .= 'INNER JOIN tmattributes a ON o.occid = a.occid ';
-			}
-			elseif(stripos($conditionSql,'s.traitid')){
-				//Search is limited by occurrence trait
-				$sql .= 'INNER JOIN tmattributes a ON o.occid = a.occid '.
-					'INNER JOIN tmstates s ON a.stateid = s.stateid ';
-			}
-			$sql .= $conditionSql.'AND d.appliedstatus = 1 '.
-				'ORDER BY o.collid';
+			$sql .= 'FROM omoccurdeterminations d INNER JOIN omoccurrences o ON d.occid = o.occid
+				INNER JOIN guidoccurdeterminations g ON d.detid = g.detid
+				LEFT JOIN taxa t ON d.tidinterpreted = t.tid ';
+			$sql .= $tableJoins;
+			$sql .= $conditionSql.' AND d.appliedstatus = 1 ';
+			$sql .= 'ORDER BY o.collid';
 			//echo '<div>'.$sql.'</div>'; exit;
 		}
 		return $sql;

classes/DwcArchiverPublisher.php

@@ -245,6 +245,7 @@ public function getDwcaItems($collid = 0){
 
 	public function getCollectionList($catID){
 		$retArr = array();
+		$serverName = $this->getDomain();
 		$sql = 'SELECT c.collid, c.collectionname, CONCAT_WS("-",c.institutioncode,c.collectioncode) as instcode, c.guidtarget, c.dwcaurl, c.managementtype, c.dynamicProperties '.
 			'FROM omcollections c INNER JOIN omcollectionstats s ON c.collid = s.collid '.
 			'LEFT JOIN omcollcatlink l ON c.collid = l.collid '.
@@ -255,8 +256,9 @@ public function getCollectionList($catID){
 		while($r = $rs->fetch_object()){
 			$retArr[$r->collid]['name'] = $r->collectionname.' ('.$r->instcode.')';
 			$retArr[$r->collid]['guid'] = $r->guidtarget;
-			$retArr[$r->collid]['url'] = substr($r->dwcaurl,0,strpos($r->dwcaurl,'/content')).'/collections/datasets/datapublisher.php';
-			$serverName = $this->getDomain();
+			$url = $r->dwcaurl;
+			if($url) $url = substr($url,0,strpos($url,'/content')).'/collections/datasets/datapublisher.php';
+			$retArr[$r->collid]['url'] = $url;
 			if(!$r->guidtarget) $retArr[$r->collid]['err'] = 'MISSING_GUID';
 			elseif($r->dwcaurl && !strpos($serverName, 'localhost') && strpos($r->dwcaurl, str_replace('www.', '', $serverName)) === false) $retArr[$r->collid]['err'] = 'ALREADY_PUB_DOMAIN';
 			if($r->dynamicProperties && strpos($r->dynamicProperties,'matSample":{"status":1')) $this->materialSampleIsActive = true;

classes/ImageShared.php

@@ -1036,8 +1036,8 @@ public static function getImgDim($imgUrl){
 		$urlPrefix .= $_SERVER["SERVER_NAME"];
 		if($_SERVER["SERVER_PORT"] && $_SERVER["SERVER_PORT"] != 80 && $_SERVER['SERVER_PORT'] != 443) $urlPrefix .= ':'.$_SERVER["SERVER_PORT"];
 
-		if(strpos($imgUrl,$urlPrefix) === 0){
-			$imgUrl = substr($imgUrl,strlen($urlPrefix));
+		if(strpos($imgUrl,$urlPrefix.$GLOBALS['IMAGE_ROOT_URL']) === 0){
+			$imgUrl = substr($imgUrl, strlen($urlPrefix));
 		}
 		if(substr($imgUrl,0,1) == '/'){
 			if($GLOBALS['IMAGE_ROOT_URL'] && strpos($imgUrl,$GLOBALS['IMAGE_ROOT_URL']) === 0){

classes/KeyDataManager.php

@@ -389,21 +389,19 @@ public function getTaxaList(){
 	public function setTaxaListSQL(){
 		if(!$this->sql){
 			if($this->clid || $this->dynClid){
-				$sqlFromBase = 'FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid '.
-					'INNER JOIN taxa t1 ON t.UnitName1 = t1.UnitName1 AND t.UnitName2 = t1.UnitName2 '.
-					'INNER JOIN taxstatus ts1 ON ts1.tidaccepted = t1.tid ';
-				$sqlWhere = 'WHERE (ts.taxauthid = 1) AND (ts1.taxauthid = 1) AND (t.RankId = 220) AND (ts.tid = ts.tidaccepted) ';
+				$sqlFromBase = 'FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid ';
+				$sqlWhere = 'WHERE (ts.taxauthid = 1) AND (t.RankId BETWEEN 180 AND 220) AND (ts.tid = ts.tidaccepted) ';
 				if($this->dynClid){
-					$sqlFromBase .= 'INNER JOIN fmdyncltaxalink clk ON ts.tid = clk.tid ';
+					$sqlFromBase .= 'INNER JOIN fmdyncltaxalink clk ON t.tid = clk.tid ';
 					$sqlWhere .= 'AND (clk.dynclid = '.$this->dynClid.') ';
 				}
 				else{
 					if($this->clType == 'dynamic'){
-						$sqlFromBase .= 'INNER JOIN omoccurrences o ON ts1.tid = o.TidInterpreted ';
+						$sqlFromBase .= 'INNER JOIN omoccurrences o ON t.tid = o.TidInterpreted ';
 						$sqlWhere .= 'AND ('.$this->dynamicSql.') ';
 					}
 					else{
-						$sqlFromBase .= 'INNER JOIN fmchklsttaxalink clk ON ts1.tid = clk.tid ';
+						$sqlFromBase .= 'INNER JOIN fmchklsttaxalink clk ON t.tid = clk.tid ';
 						$clidStr = $this->clid;
 						if($this->childClidArr){
 							$clidStr .= ','.implode(',',array_keys($this->childClidArr));
@@ -436,7 +434,6 @@ public function setTaxaListSQL(){
 					}
 				}
 				$this->sql = 'SELECT DISTINCT t.tid, ts.family, t.sciname '.$sqlFromBase.$sqlWhere;
-				//echo $this->sql;
 			}
 		}
 	}

classes/OccurrenceDataset.php

@@ -130,8 +130,9 @@ public function editDataset($dsid,$name,$notes,$description,$ispublic){
 		return true;
 	}
 
-	public function createDataset($name,$notes,$description,$ispublic,$uid){
-		$sql = 'INSERT INTO omoccurdatasets (name,notes,description,ispublic,uid) VALUES("'.$this->cleanInStr($name).'",'.($notes?'"'.$this->cleanInStr($notes).'"':'NULL').','.($description?'"'.$this->cleanInStr($description).'"':'NULL').','.($ispublic?'"'.$this->cleanInStr($ispublic).'"':'"0"').','.$uid.') ';
+	public function createDataset($name, $notes, $description, $ispublic, $uid){
+		$sql = 'INSERT INTO omoccurdatasets (name,notes,description,ispublic,uid)
+			VALUES("'.$this->cleanInStr($name).'",'.($notes?'"'.$this->cleanInStr($notes).'"':'NULL').','.($description?'"'.$this->cleanInStr($description).'"':'NULL').','.($ispublic?'"'.$this->cleanInStr($ispublic).'"':'"0"').','.$uid.') ';
 		if($this->conn->query($sql)){
 			$this->datasetId = $this->conn->insert_id;
 		}

classes/OccurrenceEditorDeterminations.php

@@ -204,7 +204,7 @@ public function deleteDetermination($detId){
 		$occid = 0;
 
 		$sql = 'SELECT occid, identifiedBy, dateIdentified, family, sciname, scientificNameAuthorship, tidInterpreted, identificationQualifier, isCurrent, printQueue,
-			appliedStatus, detType, identificationReferences, identificationRemarks, taxonRemarks, sourceIdentifier, sortSequence
+			appliedStatus, detType, identificationReferences, identificationRemarks, taxonRemarks, sortSequence
 			FROM omoccurdeterminations WHERE detid = '.$detId;
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_assoc()){

classes/OccurrenceEditorManager.php

@@ -860,25 +860,26 @@ public function editOccurrence($postArr, $editorStatus){
 				$identArr = $this->getIdentifiers($this->occid);
 				$oldValueArr = array();
 				//Get current values to be saved within versioning tables
-				$editFieldArr['occurrence'] = array_intersect($editArr,array_keys($this->fieldArr['occurrence']));
-				if($editFieldArr['occurrence']){
-					$sql = 'SELECT o.collid, '.implode(',',$editFieldArr['occurrence']).(in_array('processingstatus',$editFieldArr['occurrence'])?'':',processingstatus').
-						(in_array('recordenteredby',$editFieldArr['occurrence'])?'':',recordenteredby').' FROM omoccurrences o WHERE o.occid = '.$this->occid;
+				$editFieldArr = array();
+				$editFieldArr['omoccurrences'] = array_intersect($editArr,array_keys($this->fieldArr['occurrence']));
+				if($editFieldArr['omoccurrences']){
+					$sql = 'SELECT o.collid, '.implode(',',$editFieldArr['omoccurrences']).(in_array('processingstatus',$editFieldArr['omoccurrences'])?'':',processingstatus').
+						(in_array('recordenteredby',$editFieldArr['omoccurrences'])?'':',recordenteredby').' FROM omoccurrences o WHERE o.occid = '.$this->occid;
 					$rs = $this->conn->query($sql);
 					$oldValueArr['occurrence'] = $rs->fetch_assoc();
 					$rs->free();
 				}
 				//Get current paleo values to be saved within versioning tables
-				$editFieldArr['paleo'] = array_intersect($editArr, $this->fieldArr['paleo']);
-				if($this->paleoActivated && $editFieldArr['paleo']){
-					$sql = 'SELECT '.implode(',',$editFieldArr['paleo']).' FROM omoccurpaleo WHERE occid = '.$this->occid;
+				$editFieldArr['omoccurpaleo'] = array_intersect($editArr, $this->fieldArr['paleo']);
+				if($this->paleoActivated && $editFieldArr['omoccurpaleo']){
+					$sql = 'SELECT '.implode(',',$editFieldArr['omoccurpaleo']).' FROM omoccurpaleo WHERE occid = '.$this->occid;
 					$rs = $this->conn->query($sql);
 					if($rs->num_rows) $oldValueArr['paleo'] = $rs->fetch_assoc();
 					$rs->free();
 				}
 				//Get current identifiers values to be saved within versioning tables
-				$editFieldArr['identifier'] = array_intersect($editArr, $this->fieldArr['identifier']);
-				if($editFieldArr['identifier'] && $identArr){
+				$editFieldArr['omoccuridentifiers'] = array_intersect($editArr, $this->fieldArr['identifier']);
+				if($editFieldArr['omoccuridentifiers'] && $identArr){
 					foreach($identArr[$this->occid] as $idKey => $idArr){
 						$idStr = '';
 						if($idArr['name']) $idStr = $idArr['name'].': ';
@@ -887,8 +888,8 @@ public function editOccurrence($postArr, $editorStatus){
 					}
 				}
 				//Get current exsiccati values to be saved within versioning tables
-				$editFieldArr['exsiccati'] = array_intersect($editArr, $this->fieldArr['exsiccati']);
-				if($editFieldArr['exsiccati']){
+				$editFieldArr['omexsiccatiocclink'] = array_intersect($editArr, $this->fieldArr['exsiccati']);
+				if($editFieldArr['omexsiccatiocclink']){
 					$sql = 'SELECT et.ometid, et.title, exsnumber '.
 						'FROM omexsiccatiocclink el INNER JOIN omexsiccatinumbers en ON el.omenid = en.omenid '.
 						'INNER JOIN omexsiccatititles et ON en.ometid = et.ometid '.
@@ -919,20 +920,20 @@ public function editOccurrence($postArr, $editorStatus){
 					$oldRecordEnteredBy = isset($oldValueArr['occurrence']['recordenteredby'])?$oldValueArr['occurrence']['recordenteredby']:'';
 					if($oldRecordEnteredBy == 'preprocessed' || (!$oldRecordEnteredBy && ($oldProcessingStatus == 'unprocessed' || $oldProcessingStatus == 'stage 1'))){
 						$postArr['recordenteredby'] = $GLOBALS['USERNAME'];
-						$editFieldArr['occurrence'][] = 'recordenteredby';
+						$editFieldArr['omoccurrences'][] = 'recordenteredby';
 					}
 					//Version edits; add edits to omoccuredits
 					$sqlEditsBase = 'INSERT INTO omoccuredits(occid,reviewstatus,appliedstatus,uid,fieldname,fieldvaluenew,fieldvalueold) '.
 						'VALUES ('.$this->occid.',1,'.($autoCommit?'1':'0').','.$GLOBALS['SYMB_UID'].',';
 					foreach($editFieldArr as $tableName => $fieldArr){
-						if($tableName == 'identifier'){
+						if($tableName == 'omoccuridentifiers'){
 							if($fieldArr){
 								foreach($postArr['idkey'] as $idIndex => $idKey){
 									$newValue = $postArr['idname'][$idIndex].($postArr['idname'][$idIndex]?': ':'').$postArr['idvalue'][$idIndex];
 									$oldValue = '';
 									if(is_numeric($idKey)) $oldValue = $oldValueArr['identifier'][$idKey];
 									if($oldValue != $newValue){
-										$sqlEdit = $sqlEditsBase.'"omoccuridentifier","'.$newValue.'","'.$oldValue.'")';
+										$sqlEdit = $sqlEditsBase.'"omoccuridentifiers","'.$newValue.'","'.$oldValue.'")';
 										if(!$this->conn->query($sqlEdit)){
 											$this->errorArr[] = ''.$this->conn->error;
 										}
@@ -943,7 +944,7 @@ public function editOccurrence($postArr, $editorStatus){
 						else{
 							foreach($fieldArr as $fieldName){
 								$prefix = $tableName.':';
-								if($prefix == 'occurrence:') $prefix = '';
+								if($prefix == 'omoccurrences:') $prefix = '';
 								if(!array_key_exists($fieldName,$postArr)){
 									//Field is a checkbox that is unchecked: cultivationstatus, localitysecurity
 									$postArr[$fieldName] = 0;

collections/admin/igsnmapper.php

@@ -62,17 +62,9 @@
 <head>
 	<meta http-equiv="Content-Type" content="text/html; charset=<?php echo $CHARSET; ?>">
 	<title>IGSN GUID Mapper</title>
-  <?php
-    $activateJQuery = false;
-    if(file_exists($SERVER_ROOT.'/includes/head.php')){
-      include_once($SERVER_ROOT.'/includes/head.php');
-    }
-    else{
-      echo '<link href="'.$CLIENT_ROOT.'/css/jquery-ui.css" type="text/css" rel="stylesheet" />';
-      echo '<link href="'.$CLIENT_ROOT.'/css/base.css?ver=1" type="text/css" rel="stylesheet" />';
-      echo '<link href="'.$CLIENT_ROOT.'/css/main.css?ver=1" type="text/css" rel="stylesheet" />';
-    }
-  ?>
+	<?php
+	$activateJQuery = false;
+	include_once($SERVER_ROOT.'/includes/head.php');
 	<script type="text/javascript" src="../../js/jquery.js"></script>
 	<script type="text/javascript">
 		function validateCredentials(f){

collections/datasets/datapublisher.php

@@ -471,7 +471,7 @@ function checkAllColl(cb) {
 									if ($errMsg) $inputAttr = 'DISABLED';
 									elseif ($v['url']) $inputAttr = 'CHECKED';
 									echo '<input name="coll[]" type="checkbox" value="' . $k . '" ' . $inputAttr . ' />';
-									echo '<a href="../misc/collprofiles.php?collid=' . $k . '" target="_blank">' . $v['name'] . '</a>';
+									echo '<a href="../misc/collprofiles.php?collid=' . $k . '" target="_blank">' . $v['name'] . '</a> ';
 									if ($errMsg) echo '<span style="color:red;margin-left:15px;">' . $errMsg . '</span>';
 									elseif ($v['url']) echo '<span> - published</span>';
 									echo '<br/>';

collections/datasets/datasetHandler.php

@@ -11,29 +11,31 @@
 	$occid = array_key_exists('occid',$_POST)?$_POST['occid']:0;
 
 	//Sanitation
-	if(!is_numeric($datasetID)) $datasetID = 0;
+	if(!is_numeric($datasetID) && $datasetID != '--newDataset') $datasetID = 0;
 
 	if($action){
 		$datasetManager = new OccurrenceDataset();
 		if($datasetID == '--newDataset'){
 			$name = 'newDataset ('.date('Y-m-d H:i:s').')';
-			$datasetManager->createDataset($name,'','','',$SYMB_UID);
-			$datasetID = $datasetManager->getDatasetId();
+			if($datasetManager->createDataset($name, '', '', '', $SYMB_UID)) $datasetID = $datasetManager->getDatasetId();
+			else echo $datasetManager->getErrorMessage();
 		}
 		$targetLink = 'datasetmanager.php?datasetid='.$datasetID;
 		if($sourcePage == 'individual') $targetLink = '../individual/index.php?occid='.$occid;
-		if($action == 'addSelectedToDataset'){
-			if($occid){
-				if($datasetManager->addSelectedOccurrences($datasetID, $occid)){
-					header('Location: '.$targetLink);
+		if($datasetID){
+			if($action == 'addSelectedToDataset'){
+				if($occid){
+					if($datasetManager->addSelectedOccurrences($datasetID, $occid)){
+						header('Location: '.$targetLink);
+					}
+					else echo $datasetManager->getErrorMessage();
 				}
-				else echo $datasetManager->getErrorMessage();
 			}
-		}
-		elseif($action == 'addAllToDataset'){
-			$occurManager = new OccurrenceManager('write');
-			if($occurManager->addOccurrencesToDataset($datasetID)) header('Location: '.$targetLink);
-			else echo $occurManager->getErrorMessage();
+			elseif($action == 'addAllToDataset'){
+				$occurManager = new OccurrenceManager('write');
+				if($occurManager->addOccurrencesToDataset($datasetID)) header('Location: '.$targetLink);
+				else echo $occurManager->getErrorMessage();
+			}
 		}
 	}
 }