sync tyrrell-dev with tyrrell-master (local)

checklists/checklist.php

@@ -107,18 +107,14 @@
 		if($clid) echo 'var clid = '.$clid.';'."\n";
 		echo 'var taxaCount = '.count($taxaArray).';'."\n";
 		?>
-		$( function() {
-			$( document ).tooltip();
-		} );
-
 		function changeImageSource(elem){
 			let f = document.optionform;
 			if(elem.id == "vi_voucher") f.voucherimages.value = "1";
 			else f.voucherimages.value = "0";
 			f.submit();
 		}
 	</script>
-	<script type="text/javascript" src="../js/symb/checklists.checklist.js?ver=3"></script>
+	<script type="text/javascript" src="../js/symb/checklists.checklist.js?ver=4"></script>
 	<style type="text/css">
 		<?php
 		if($printMode){

checklists/checklistadminmeta.php

@@ -122,6 +122,19 @@ function openMappingPolyAid() {
 		mapWindow=open("<?php echo $CLIENT_ROOT; ?>/checklists/tools/mappolyaid.php?clid=<?php echo $clid; ?>&formname=editclmatadata&latname=latcentroid&longname=longcentroid&latdef="+latDec+"&lngdef="+lngDec,"mapaid","resizable=0,width=1000,height=800,left=20,top=20");
 	    if(mapWindow.opener == null) mapWindow.opener = self;
 	}
+
+	function enableDisableExtServiceFields() {
+		let xsrv = document.getElementById('externalservice');
+		let xsid = document.getElementById('externalserviceid');
+		let xstaxonfilter = document.getElementById('externalserviceiconictaxon');
+		if(xsrv.value == '') {
+			xsid.setAttribute("disabled","");
+			xstaxonfilter.setAttribute("disabled","");
+		} else {
+			xsid.removeAttribute("disabled");
+			xstaxonfilter.removeAttribute("disabled");
+		}
+	}
 </script>
 <?php
 if(!$clid){
@@ -180,7 +193,7 @@ function openMappingPolyAid() {
 			</div>
 			<div>
 				<b><?php echo (isset($LANG['EXTSERVICE'])?$LANG['EXTSERVICE']:'External Service (e.g., iNaturalist) to associate with this checklist [optional]');?></b><br/>
-				<select name="externalservice">
+				<select name="externalservice" id="externalservice" onchange="enableDisableExtServiceFields()">
 					<option value=""></option>
 					<option value="">-------------------------------</option>
 					<option value="inaturalist" <?php echo (($dynamPropsArr['externalservice']=='inaturalist')?'selected':''); ?>>iNaturalist</option>
@@ -189,10 +202,10 @@ function openMappingPolyAid() {
 			<div style="width:100%;margin-top:5px">
 				<div style="float:left;width:25%">
 				<b><?php echo (isset($LANG['EXTSERVICEID'])?$LANG['EXTSERVICEID']:'Project ID from External Service');?></b><br/>
-				<input type="text" name="externalserviceid" style="width:100%" value="<?php echo ($dynamPropsArr?$dynamPropsArr['externalserviceid']:''); ?>" />
+				<input type="text" name="externalserviceid" id="externalserviceid" style="width:100%" value="<?php echo ($dynamPropsArr?$dynamPropsArr['externalserviceid']:''); ?>" />
 				</div><div style="float:left;margin-left:15px;">
 				<b><?php echo (isset($LANG['EXTSERVICETAXON'])?$LANG['EXTSERVICETAXON']:'External Service Taxon Filter [optional]');?></b><br/>
-				<input type="text" name="externalserviceiconictaxon" style="width:100%" value="<?php echo ($dynamPropsArr?$dynamPropsArr['externalserviceiconictaxon']:''); ?>" />
+				<input type="text" name="externalserviceiconictaxon" id="externalserviceiconictaxon" style="width:100%" value="<?php echo ($dynamPropsArr?$dynamPropsArr['externalserviceiconictaxon']:''); ?>" />
 				</div>
 			</div>
 			<div id="locDiv" style="clear:both;margin-top:5px;">

checklists/checklistmap.php

@@ -85,7 +85,7 @@ function initialize(){
 			}
 			$clMeta = $clManager->getClMetaData();
 			//Check for and add checklist polygon
-			$clMeta = $clManager->getClMetaData();
+
 			if($clMeta['footprintwkt']){
 				//Add checklist polygon
 				$wkt = $clMeta['footprintwkt'];

checklists/externalvouchers.php

@@ -0,0 +1,132 @@
+<?php
+include_once('../config/symbini.php');
+include_once($SERVER_ROOT.'/classes/ChecklistVoucherReport.php');
+include_once($SERVER_ROOT.'/classes/ChecklistManager.php');
+include_once($SERVER_ROOT.'/content/lang/checklists/voucheradmin.'.$LANG_TAG.'.php');
+
+$clid = array_key_exists('clid', $_REQUEST) ? filter_var($_REQUEST['clid'], FILTER_SANITIZE_NUMBER_INT) : 0;
+$pid = array_key_exists('pid', $_REQUEST) ? filter_var($_REQUEST['pid'], FILTER_SANITIZE_NUMBER_INT) : '';
+$startPos = (array_key_exists('start', $_REQUEST) ? filter_var($_REQUEST['start'], FILTER_SANITIZE_NUMBER_INT) : 0);
+$displayMode = (array_key_exists('displaymode', $_REQUEST) ? filter_var($_REQUEST['displaymode'], FILTER_SANITIZE_NUMBER_INT) : 0);
+
+$clManager = new ChecklistManager();
+$clVoucherManager = new ChecklistVoucherReport();
+if($clid) {
+	$clManager->setClid($clid);
+	$clVoucherManager->setClid($clid);
+	//$clVoucherManager->setCollectionVariables();
+}
+
+$isEditor = 0;
+if($IS_ADMIN || (array_key_exists('ClAdmin', $USER_RIGHTS) && in_array($clid, $USER_RIGHTS['ClAdmin']))){
+	$isEditor = 1;
+}
+if($isEditor){
+	$taxaArray = $clManager->getTaxaList();
+	?>
+	<div id="externalServiceVoucherDiv">
+    <div style="margin:10px;">
+    <div style="clear:both;">
+		<div style="margin:10px;">
+			<?php echo $LANG['LISTEDBELOWEXTERNAL'];?>
+		</div>
+		<div style="margin:20px;">
+		<style>
+			#taxalist-div {
+				margin-bottom: 10px;
+			}
+			label {
+				display: inline-block;
+				width: 250px;
+				text-align: right;
+			}
+		</style>
+			<?php
+			echo '<div id="taxalist-div">';
+			$prevGroup = '';
+			foreach($taxaArray as $tid => $sppArr){
+				$group = $sppArr['taxongroup'];
+				if($group != $prevGroup){
+					$famUrl = '../taxa/index.php?taxauthid=1&taxon='.strip_tags($group).'&clid='.$clid;
+					//Edit family name display style here
+					?>
+					<div class="family-div" id="<?php echo strip_tags($group);?>">
+						<a href="<?php echo $famUrl; ?>" target="_blank" style="color:black;"><?php echo $group;?></a>
+					</div>
+					<?php
+					$prevGroup = $group;
+				}
+				$taxonWithDashes = str_replace(' ', '-', $sppArr['sciname']);
+				echo '<div class="taxon-container">';
+				echo '<a href="#" target="_blank" id="a-' . $taxonWithDashes . '" style="pointer-events:none;">'; 
+				echo '<label>'.$sppArr['sciname'].' '.$sppArr["author"].'</label></a>&nbsp;';
+				//class="taxon-span" 
+				?>
+				<input type="text" name="<?php echo $tid; ?>" id="i-<?php echo $taxonWithDashes; ?>">
+				<span class="view-specimen-span printoff">
+					<a href="#" target="_blank" style="text-decoration: none;">
+						<img src="../images/link.png" style="width:12px;" title="<?php echo (isset($LANG['LINKEXT'])?$LANG['LINKEXT']:'Link external vouchers'); ?>" />
+					</a>
+				</span>
+				<?php
+				echo "</div>\n";
+				$scinameasid = str_replace(" ", "-", $sppArr['sciname']);
+				if($arrforexternalserviceapi == '') {
+					$arrforexternalserviceapi .= "'" . $scinameasid . "'";
+				} else {
+					$arrforexternalserviceapi .= ",'" . $scinameasid . "'";
+				}
+			}
+			echo '</div>';
+			//if(isset($dynamPropsArr) && $dynamPropsArr['externalservice'] == 'inaturalist') {
+				echo '<script src="../js/symb/checklists.externalserviceapi.js"></script>';
+				?>
+				<script>
+					<?php 
+					echo 'const checklisttaxa = [' . $arrforexternalserviceapi . '];';
+					//echo 'const externalProjID = "' . ($dynamPropsArr['externalserviceid']?$dynamPropsArr['externalserviceid']:'') . '";';
+					echo 'const externalProjID = "biodiversity-of-puerto-rico";'; //DEBUG ONLY!!!!!!!!!!!!!
+					echo 'const iconictaxon = "' . ($dynamPropsArr['externalserviceiconictaxon']?$dynamPropsArr['externalserviceiconictaxon']:'') . '";';
+					?>
+
+					// iNaturalist Integration
+					// Note: the two part request (...Page1 vs ...AdditionalPages) is performed
+					// to allow for a variable number of total results. There will always be a 
+					// first page, but there may be 0 or more additional pages. The answer is
+					// extracted from the response to the first ("Page1") fetch request.
+					fetchiNatPage1(externalProjID, iconictaxon)
+						.then(pageone => {
+							const totalresults = pageone.total_results;
+							const perpage = pageone.per_page;
+							const loopnum = Math.ceil(totalresults / perpage);
+							const taxalist1 = extractiNatTaxaIdAndName(pageone.results);
+							fetchiNatAdditionalPages(loopnum, externalProjID, iconictaxon)
+							.then(pagestwoplus => {
+								const taxalist2 = pagestwoplus.map(page => extractiNatTaxaIdAndName(page.results))
+								taxalist = taxalist1.concat(taxalist2.flat());
+								checklisttaxa.forEach( taxon => { 
+									let anchortag = document.getElementById('a-'+taxon);
+									let imgtag = document.getElementById('i-'+taxon);
+									let taxonwithspaces = taxon.replaceAll('-', ' ');
+									const idx = taxalist.findIndex( elem => elem.name === taxonwithspaces);
+									if(idx >= 0) {
+										console.log('yep');
+										anchortag.setAttribute("style", "pointer-events:auto;");
+										imgtag.setAttribute("style", "background-color: #f1e740;");
+										anchortag.setAttribute("href", `https://www.inaturalist.org/observations?project_id=${externalProjID}&taxon_id=${taxalist[idx].id}`);
+									}
+								})
+							})
+							.catch(error => {
+								error.message;
+							})
+						})
+				</script>
+			<?php //} ?>
+		</div>
+    </div>
+	</div>
+    </div>
+	<?php
+}
+?>

checklists/rpc/searchsuggest.php

@@ -1,13 +1,13 @@
 <?php
 include_once('../../config/symbini.php');
 include_once($SERVER_ROOT.'/classes/ChecklistManager.php');
-header("Content-Type: text/html; charset=".$CHARSET);
+header('Content-Type: text/html; charset='.$CHARSET);
 
 $clid = $_REQUEST['clid'];
 $term = $_REQUEST['term'];
 $deep = (isset($_REQUEST['deep'])?$_REQUEST['deep']:0);
 
 $clManager = new ChecklistManager();
-$retArr = $clManager->getTaxonSearch($term,$clid,$deep);
+$retArr = $clManager->getTaxonSearch($term, $clid, $deep);
 echo json_encode($retArr);
 ?>

checklists/voucheradmin.php

@@ -235,7 +235,8 @@
 				<li><a href="nonvoucheredtab.php?clid=<?php echo $clid.'&pid='.$pid.'&start='.$startPos.'&displaymode='.$displayMode; ?>"><span><?php echo $LANG['NON_VOUCHERED'];?></span></a></li>
 				<li><a href="vamissingtaxa.php?clid=<?php echo $clid.'&pid='.$pid.'&start='.$startPos.'&displaymode='.($tabIndex==1?$displayMode:0).'&excludevouchers='.(isset($_POST['excludevouchers'])?$_POST['excludevouchers']:''); ?>"><span><?php echo $LANG['MISSINGTAXA'];?></span></a></li>
 				<li><a href="vaconflicts.php?clid=<?php echo $clid.'&pid='.$pid.'&start='.$startPos; ?>"><span><?php echo $LANG['VOUCHCONF'];?></span></a></li>
-				<?php
+				<?php 
+				if($clManager->getAssociatedExternalService()) echo '<li><a href="externalvouchers.php?clid='.$clid.'&pid='.$pid.'&start='.$startPos.'"><span>' . $LANG['EXTVOUCH'] . '</span></a></li>';
 				if($clManager->hasVoucherProjects()) echo '<li><a href="imgvouchertab.php?clid='.$clid.'">'.(isset($LANG['ADDIMGV'])?$LANG['ADDIMGV']:'Add Image Voucher').'</a></li>';
 				?>
 				<li><a href="#reportDiv"><span><?php echo $LANG['REPORTS'];?></span></a></li>

classes/ChecklistManager.php

@@ -330,11 +330,16 @@ private function setImages(){
 		if($this->taxaList){
 			$matchedArr = array();
 			if($this->limitImagesToVouchers){
+				$clidStr = $this->clid;
+				if($this->childClidArr){
+					$clidStr .= ','.implode(',',array_keys($this->childClidArr));
+				}
 				$sql = 'SELECT i.tid, i.url, i.thumbnailurl, i.originalurl
 					FROM images i INNER JOIN omoccurrences o ON i.occid = o.occid
 					INNER JOIN fmvouchers v ON o.occid = v.occid
 					INNER JOIN fmchklsttaxalink cl ON v.clTaxaID = cl.clTaxaID
-					WHERE (cl.clid = 2) AND (i.tid IN('.implode(',',array_keys($this->taxaList)).'))';
+					WHERE (cl.clid = '.$clidStr.') AND (i.tid IN('.implode(',',array_keys($this->taxaList)).'))
+					ORDER BY i.sortOccurrence, i.sortSequence';
 				$matchedArr = $this->setImageSubset($sql);
 			}
 			if($missingArr = array_diff(array_keys($this->taxaList),$matchedArr)){
@@ -347,7 +352,7 @@ private function setImages(){
 				$matchedArr = $this->setImageSubset($sql);
 				if($missingArr = array_diff(array_keys($this->taxaList),$matchedArr)){
 					//Get children images
-					$sql = 'SELECT i2.tid, i.url, i.thumbnailurl FROM images i INNER JOIN '.
+					$sql = 'SELECT DISTINCT i2.tid, i.url, i.thumbnailurl FROM images i INNER JOIN '.
 						'(SELECT ts1.parenttid AS tid, SUBSTR(MIN(CONCAT(LPAD(i.sortsequence,6,"0"),i.imgid)),7) AS imgid '.
 						'FROM taxstatus ts1 INNER JOIN taxstatus ts2 ON ts1.tidaccepted = ts2.tidaccepted '.
 						'INNER JOIN images i ON ts2.tid = i.tid '.
@@ -362,7 +367,6 @@ private function setImages(){
 	private function setImageSubset($sql){
 		$matchTidArr = array();
 		if($this->taxaList){
-			//echo $sql;
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
 				if(!in_array($r->tid,$matchTidArr)){

classes/ChecklistVoucherAdmin.php

@@ -44,7 +44,7 @@ public function setClid($clid){
 	private function setMetaData(){
 		if($this->clid){
 			$sql = 'SELECT clid, name, locality, publication, abstract, authors, parentclid, notes, latcentroid, longcentroid, pointradiusmeters, '.
-				'footprintwkt, access, defaultSettings, dynamicsql, datelastmodified, uid, type, initialtimestamp '.
+				'footprintwkt, access, defaultSettings, dynamicsql, datelastmodified, dynamicProperties, uid, type, initialtimestamp '.
 				'FROM fmchecklists WHERE (clid = '.$this->clid.')';
 		 	$rs = $this->conn->query($sql);
 			if($rs){
@@ -66,6 +66,7 @@ private function setMetaData(){
 					$this->clMetadata["defaultSettings"] = $row->defaultSettings;
 					$this->clMetadata["dynamicsql"] = $row->dynamicsql;
 					$this->clMetadata["datelastmodified"] = $row->datelastmodified;
+					$this->clMetadata['dynamicProperties'] = $row->dynamicProperties;
 				}
 				$rs->free();
 			}
@@ -108,6 +109,17 @@ public function getPolygonCoordinates(){
 		return $retArr;
 	}
 
+	public function getAssociatedExternalService(){
+		$resp = 'FALSE';
+ 		if($this->clMetadata['dynamicProperties']){
+			$dynpropArr = json_decode($this->clMetadata['dynamicProperties'], TRUE);
+			if(array_key_exists('externalservice', $dynpropArr)) {
+				$resp = $dynpropArr['externalservice'];
+			}
+		} 
+		return $resp;
+	}
+
 	//Dynamic query variable functions
 	public function setCollectionVariables(){
 		if($this->clid){

classes/DwcArchiverCore.php

@@ -43,7 +43,7 @@ class DwcArchiverCore extends Manager{
 	private $includeDets = 1;
 	private $includeImgs = 1;
 	private $includeAttributes = 0;
-	private $includeMaterialSample = 0;		// 0 = off, 1 = on, 2 = active (activated within at least one collection)
+	private $includeMaterialSample = 0;
 	private $hasPaleo = false;
 	private $redactLocalities = 1;
 	private $rareReaderArr = array();
@@ -191,7 +191,6 @@ public function setCollArr($collTarget, $collType = ''){
 									if (isset($modArr['paleo']['status'])) $this->hasPaleo = true;
 									elseif (isset($modArr['matSample']['status'])){
 										$this->collArr[$r->collid]['matSample'] = 1;
-										$this->includeMaterialSample = 2;
 									}
 								}
 							}
@@ -1055,7 +1054,7 @@ private function writeMetaFile(){
 		}
 
 		//MaterialSample extension
-		if ($this->includeMaterialSample == 2 && isset($this->fieldArrMap['materialSample'])) {
+		if ($this->includeMaterialSample && isset($this->fieldArrMap['materialSample'])) {
 			$extElem3 = $newDoc->createElement('extension');
 			$extElem3->setAttribute('encoding', $this->charSetOut);
 			$extElem3->setAttribute('fieldsTerminatedBy', $this->delimiter);
@@ -1765,7 +1764,7 @@ private function writeOccurrenceFile(){
 
 				$batchOccidArr[] = $r['occid'];
 				if (count($batchOccidArr) > 1000) {
-					if ($this->includeMaterialSample == 2) $this->writeMaterialSampleData($materialSampleHandler, $batchOccidArr);
+					if ($this->includeMaterialSample) $this->writeMaterialSampleData($materialSampleHandler, $batchOccidArr);
 					if ($pubID && $portalManager) $portalManager->insertPortalOccurrences($pubID, $batchOccidArr);
 					unset($batchOccidArr);
 					$batchOccidArr = array();
@@ -1782,7 +1781,7 @@ private function writeOccurrenceFile(){
 			if ($batchOccidArr) {
 				if ($pubID && $portalManager) $portalManager->insertPortalOccurrences($pubID, $batchOccidArr);
 			}
-			if ($this->includeMaterialSample == 2){
+			if ($this->includeMaterialSample){
 				$this->writeMaterialSampleData($materialSampleHandler, $batchOccidArr);
 				$materialSampleHandler->__destruct();
 			}
@@ -1801,7 +1800,7 @@ private function writeOccurrenceFile(){
 			$this->logOrEcho($this->errorMessage);
 		}
 		$this->logOrEcho('Done! (' . date('h:i:s A') . ")\n");
-		if ($this->includeMaterialSample == 2) $this->logOrEcho('Material Sample extension file created (' . date('h:i:s A') . ')... ');
+		if ($this->includeMaterialSample) $this->logOrEcho('Material Sample extension file created (' . date('h:i:s A') . ')... ');
 		return $filePath;
 	}
 
@@ -2161,19 +2160,19 @@ public function setDelimiter($d){
 	}
 
 	public function setIncludeDets($includeDets){
-		$this->includeDets = $includeDets;
+		if($includeDets) $this->includeDets = true;
 	}
 
 	public function setIncludeImgs($includeImgs){
-		$this->includeImgs = $includeImgs;
+		if($includeImgs) $this->includeImgs = true;
 	}
 
 	public function setIncludeAttributes($include){
-		$this->includeAttributes = $include;
+		if($include) $this->includeAttributes = true;
 	}
 
 	public function setIncludeMaterialSample($include){
-		$this->includeMaterialSample = $include;
+		if($include) $this->includeMaterialSample = true;
 	}
 
 	public function hasAttributes(){