Hotfix 2023 07 22 (BioKIC#559)

* Hotfix - 2023-07-22 - DwcArchivePublishing: Material Sample publishing bug - DwC-A upload: Scientific name failed to be built when taxonomic data is supplied by by individual components - Taxonomic autocomplete: Allow autocomplete handle apostrophes - Checklist Display: Bug fix that interfered with display of linked voucher images - Checklist Manager: Checklist taxon search autocomplete failed to include higher taxa (parent data) - Taxonomy Harvester bug: F-dex harvest failed to grab parents when source was not "Index Fungorum" - Specimen Upload: Set version data changes as the default action only when a collection is live managed - Occurrence Search Harvest: Reworked search form validation to be more efficient; Fix bug with occurrence attribute checkbox/radio failing to be recognized as a selected component * Hotfix 2023-06-19 (BioKIC#518) - Taxonomy Harvesting: Don't check following taxonomic resource on a positive match and input; synchronize display text - Refactor ImageLocalProcessor: -- Provide support for input file to include medium and thumbnail image derivatives -- Expand Image Map processing to allow mapping file to include any images table field name -- Expand images insert function to handle any valid field found within images table -- MD5 hash large version of image input file, but don't overwrite hash if supplied by source -- Handle BOM characters at start of csv file. -- Trim header elements for testing column names. -- Enforce default action of accepting derivative urls supplied within a csv image map file -- Make sure to remove staging images - Occurrence Public Display: Allow occurrence archive (deleted occurrences) to be searchable by GUID (occurrenceID, recordID), thus reporting when a record is deleted - Checklist multi-polygon Map: resolve Multipolygons failing to map within both simple and dynamic maps - Occurrence Reviewer: Fix for field name and start and end date filter variables failing to be carried forward when advancing to pages beyond 1000 records - Collection metadata editor: Reset contact array to ensure that JSON string is standardized as a non-associated array --------- Co-authored-by: Greg Post <[email protected]>
CCH2-org · Jul 29, 2023 · b3bccdb · b3bccdb
1 parent deb6549
commit b3bccdb
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Showing 15 changed files with 80 additions and 96 deletions.
diff --git a/checklists/checklist.php b/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){

diff --git a/checklists/rpc/searchsuggest.php b/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);
 ?>
diff --git a/classes/ChecklistManager.php b/classes/ChecklistManager.php
@@ -329,11 +329,16 @@ 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)){
@@ -346,7 +351,7 @@ 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 '.
+					$sql = 'SELECT DISTINCT i2.tid, i.url, i.thumbnailurl FROM images i INNER JOIN '.
 						'(SELECT ts1.parenttid AS tid, SUBSTR(MIN(CONCAT(LPAD(i.sortsequence,6,"0"),i.imgid)),7) AS imgid '.
 						'FROM taxstatus ts1 INNER JOIN taxstatus ts2 ON ts1.tidaccepted = ts2.tidaccepted '.
 						'INNER JOIN images i ON ts2.tid = i.tid '.
@@ -361,7 +366,6 @@ private function setImages(){
 	private function setImageSubset($sql){
 		$matchTidArr = array();
 		if($this->taxaList){
-			//echo $sql;
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
 				if(!in_array($r->tid,$matchTidArr)){

diff --git a/classes/DwcArchiverCore.php b/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(){

diff --git a/classes/OccurrenceUtilities.php b/classes/OccurrenceUtilities.php
@@ -704,11 +704,13 @@ public static function occurrenceArrayCleaning($recMap){
 			}
 		}
 		else{
-			if(array_key_exists('genus',$recMap) && array_key_exists('specificepithet',$recMap) && array_key_exists('infraspecificepithet',$recMap)){
+			if(array_key_exists('genus',$recMap) && array_key_exists('specificepithet',$recMap)){
 				//Build sciname from individual units supplied by source
 				$sciName = trim($recMap['genus'].' '.$recMap['specificepithet']);
-				if(array_key_exists('taxonrank',$recMap)) $sciName .= ' '.$recMap['taxonrank'];
-				$sciName .= ' '.$recMap['infraspecificepithet'];
+				if(array_key_exists('infraspecificepithet',$recMap)){
+					if(array_key_exists('taxonrank',$recMap)) $sciName .= ' '.$recMap['taxonrank'];
+					$sciName .= ' '.$recMap['infraspecificepithet'];
+				}
 				$recMap['sciname'] = trim($sciName);
 			}
 			elseif(array_key_exists('scientificname',$recMap)){

diff --git a/classes/SpecUploadDwca.php b/classes/SpecUploadDwca.php
@@ -601,10 +601,8 @@ public function uploadData($finalTransfer){
 									$index = array_shift($indexArr);
 									if(array_key_exists($index,$recordArr)){
 										$valueStr = trim($recordArr[$index]);
-										if($valueStr){
-											if($cset != $this->encoding) $valueStr = $this->encodeString($valueStr);
-											$recMap[$symbField] = $valueStr;
-										}
+										if($cset != $this->encoding) $valueStr = $this->encodeString($valueStr);
+										$recMap[$symbField] = $valueStr;
 									}
 								}
 							}

diff --git a/classes/TaxonSearchSupport.php b/classes/TaxonSearchSupport.php
@@ -99,7 +99,7 @@ private function getTaxaSuggestByRank(){
 	//Setters and getters
 	public function setQueryString($queryString){
 		//$queryString = $this->cleanInStr($queryString);
-		$queryString = preg_replace('/[\'"+\-=@$%]+/i', '', $queryString);
+		$queryString = preg_replace('/[\'"+\=@$%]+/i', '', $queryString);
 		if(strpos($queryString, ' ')){
 			$queryString = preg_replace('/\s{1}x{1}$/i', ' _', $queryString);
 			$queryString = preg_replace('/\s{1}x{1}\s{1}/i', ' _ ', $queryString);

diff --git a/classes/TaxonomyHarvester.php b/classes/TaxonomyHarvester.php
@@ -965,28 +965,26 @@ private function addFdexTaxon($taxonArr){
 				if($numResults){
 					$tidAccepted = 0;
 					foreach($resultArr as $unitArr){
-						if($unitArr['recordSource'] == 'Index Fungorum'){
-							$taxonArr['sciname'] = $unitArr['taxon'];
-							$taxonArr['author'] = $unitArr['authors'];
-							$rankID = $this->getRankId($unitArr['rank']);
-							if($rankID) $taxonArr['rankid'] = $rankID;
-							$taxonArr['source'] = 'Via fDex: '.$unitArr['recordSource'];
-							$taxonArr['notes'] = 'taxonomicStatus: '.$unitArr['taxonomicStatus'].'; currentStatus: '.$unitArr['currentStatus'];
-							if(isset($unitArr['parentTaxon'])){
-								$parentTaxon = $unitArr['parentTaxon'];
-								$parentTid = 0;
-								$parentArr = $this->parseCleanCheck($parentTaxon);
-								if(isset($parentArr['tid']) && $parentArr['tid']) $parentTid = $parentArr['tid'];
-								else $parentTid = $this->addFdexTaxon($parentArr);
-								if($parentTid) $taxonArr['parent']['tid'] = $parentTid;
-							}
-							if($unitArr['taxon'] != $unitArr['currentTaxon']){
-								$acceptedArr = $this->parseCleanCheck($unitArr['currentTaxon']);
-								if(isset($acceptedArr['tid']) && $acceptedArr['tid']) $tidAccepted = $acceptedArr['tid'];
-								else $tidAccepted = $this->addFdexTaxon($acceptedArr);
-							}
+						$taxonArr['sciname'] = $unitArr['taxon'];
+						$taxonArr['author'] = $unitArr['authors'];
+						$rankID = $this->getRankId($unitArr['rank']);
+						if($rankID) $taxonArr['rankid'] = $rankID;
+						$taxonArr['source'] = 'Via fDex: '.$unitArr['recordSource'];
+						$taxonArr['notes'] = 'taxonomicStatus: '.$unitArr['taxonomicStatus'].'; currentStatus: '.$unitArr['currentStatus'];
+						if(isset($unitArr['parentTaxon'])){
+							$parentTaxon = $unitArr['parentTaxon'];
+							$parentTid = 0;
+							$parentArr = $this->parseCleanCheck($parentTaxon);
+							if(isset($parentArr['tid']) && $parentArr['tid']) $parentTid = $parentArr['tid'];
+							else $parentTid = $this->addFdexTaxon($parentArr);
+							if($parentTid) $taxonArr['parent']['tid'] = $parentTid;
 						}
-						break;
+						if($unitArr['taxon'] != $unitArr['currentTaxon']){
+							$acceptedArr = $this->parseCleanCheck($unitArr['currentTaxon']);
+							if(isset($acceptedArr['tid']) && $acceptedArr['tid']) $tidAccepted = $acceptedArr['tid'];
+							else $tidAccepted = $this->addFdexTaxon($acceptedArr);
+						}
+						if($unitArr['recordSource'] == 'Index Fungorum') break;
 					}
 					if($taxonArr) $tid = $this->loadNewTaxon($taxonArr, $tidAccepted);
 				}

diff --git a/collections/admin/specuploadmap.php b/collections/admin/specuploadmap.php
@@ -627,9 +627,11 @@ function pkChanged(selObj){
 								</ul>
 								<?php
 							}
+							$versionCheckedStr = '';
+							if($isLiveData) $versionCheckedStr = 'checked';
 							?>
 							<div style="margin:10px 0px;">
-								<input name="versiondata" type="checkbox" value="1" checked />
+								<input name="versiondata" type="checkbox" value="1" <?php echo $versionCheckedStr; ?> />
 								<?php echo (isset($LANG['VERSION_DATA_CHANGES'])?$LANG['VERSION_DATA_CHANGES']:'Version data changes'); ?>
 							</div>
 							<div style="margin:10px 0px;">

diff --git a/collections/harvestparams.php b/collections/harvestparams.php
@@ -7,7 +7,6 @@
 
 $collManager = new OccurrenceManager();
 $searchVar = $collManager->getQueryTermStr();
-$attribSearch = new OccurrenceAttributeSearch();
 ?>
 <html>
 <head>
@@ -19,7 +18,7 @@
 	<script src="../js/jquery-3.2.1.min.js?ver=3" type="text/javascript"></script>
 	<script src="../js/jquery-ui/jquery-ui.min.js?ver=3" type="text/javascript"></script>
 	<link href="../js/jquery-ui/jquery-ui.min.css" type="text/css" rel="Stylesheet" />
-	<script src="../js/symb/collections.harvestparams.js?ver=1" type="text/javascript"></script>
+	<script src="../js/symb/collections.harvestparams.js?ver=2" type="text/javascript"></script>
 	<script src="../js/symb/collections.traitsearch.js?ver=8" type="text/javascript"></script> <!-- Contains search-by-trait modifications -->
 	<script src="../js/symb/wktpolygontools.js?ver=1c" type="text/javascript"></script>
 	<script type="text/javascript">
@@ -244,7 +243,8 @@
 				</div>
 			</div>
 			<?php
-			if(isset($SEARCH_BY_TRAITS) && $SEARCH_BY_TRAITS) {
+			if(!empty($SEARCH_BY_TRAITS)) {
+				$attribSearch = new OccurrenceAttributeSearch();
 				$traitArr = $attribSearch->getTraitSearchArr($SEARCH_BY_TRAITS);
 				if($traitArr){
 					?>

diff --git a/config/symbbase.php b/config/symbbase.php
@@ -2,7 +2,7 @@
 header('X-Frame-Options: DENY');
 header('Cache-control: private'); // IE 6 FIX
 date_default_timezone_set('America/Phoenix');
-$CODE_VERSION = '3.0.10';
+$CODE_VERSION = '3.0.11';
 
 if(!isset($CLIENT_ROOT) && isset($clientRoot)) $CLIENT_ROOT = $clientRoot;
 if(substr($CLIENT_ROOT,-1) == '/') $CLIENT_ROOT = substr($CLIENT_ROOT,0,strlen($CLIENT_ROOT)-1);

diff --git a/config/symbini_template.php b/config/symbini_template.php
@@ -73,8 +73,8 @@
 $ACTIVATE_DUPLICATES = 0;			//Activates Specimen Duplicate listings and support features. Mainly relavent for herabrium collections
 $ACTIVATE_EXSICCATI = 0;			//Activates exsiccati fields within data entry pages; adding link to exsiccati search tools to portal menu is recommended
 $ACTIVATE_GEOLOCATE_TOOLKIT = 0;	//Activates GeoLocate Toolkit located within the Processing Toolkit menu items
-$SEARCH_BY_TRAITS = '0';			//Activates search fields for searching by traits (if trait data have been encoded): 0 = trait search off; any number of non-zeros separated by commas (e.g., '1,6') = trait search on for the traits with these id numbers in table tmtraits.
-$CALENDAR_TRAIT_PLOTS = '0';			//Activates polar plots, in taxon profile, of the trait states listed: 0 = no plot; any number of non-zeros separated by commas (e.g., '1,6') = plots appear for the trait states with these id numbers (in table tmstates).
+$SEARCH_BY_TRAITS = 0;			//Activates search fields for searching by traits (if trait data have been encoded): 0 = trait search off; any number of non-zeros separated by commas (e.g., '1,6') = trait search on for the traits with these id numbers in table tmtraits.
+$CALENDAR_TRAIT_PLOTS = 0;			//Activates polar plots, in taxon profile, of the trait states listed: 0 = no plot; any number of non-zeros separated by commas (e.g., '1,6') = plots appear for the trait states with these id numbers (in table tmstates).
 
 $IGSN_ACTIVATION = 0;
 

diff --git a/js/symb/checklists.checklist.js b/js/symb/checklists.checklist.js
@@ -2,7 +2,7 @@ $(document).ready(function() {
 	//Filter autocomplete
 	$("#taxonfilter").autocomplete({ 
 		source: function( request, response ) {
-			$.getJSON( "rpc/searchsuggest.php", { term: request.term, clid: clid }, response );
+			$.getJSON( "rpc/searchsuggest.php", { term: request.term, clid: clid, deep: 1 }, response );
 		}
 	},
 	{ minLength: 3 });
@@ -17,11 +17,6 @@ $(document).ready(function() {
 		autoFocus: true
 	});
 
-	$("#speciestoadd").autocomplete({
-		source: "rpc/speciessuggest.php",
-		minLength: 4,
-		autoFocus: true
-	});
 	if(document.cookie.indexOf("editspp") > -1){
 		$(".editspp").show();
 		document.getElementById("editsppon").style.display = "inline";

diff --git a/js/symb/collections.harvestparams.js b/js/symb/collections.harvestparams.js
@@ -13,37 +13,27 @@ function cleanNumericInput(formElem){
 
 function checkHarvestParamsForm(frm){
 	//make sure they have filled out at least one field.
-	if((frm.taxa.value.trim() == '') && (frm.country.value.trim() == '') && (frm.state.value.trim() == '') && (frm.county.value.trim() == '') &&
-		(frm.local.value.trim() == '') && (frm.elevlow.value.trim() == '') && (frm.upperlat.value.trim() == '') && (frm.footprintwkt.value.trim() == '') && (frm.pointlat.value.trim() == '') &&
-		(frm.collector.value.trim() == '') && (frm.collnum.value.trim() == '') && (frm.eventdate1.value.trim() == '') && (frm.catnum.value.trim() == '') &&
-		(frm.typestatus.checked == false) && (frm.hasimages.checked == false) && (frm.hasgenetic.checked == false) && (frm.hascoords.checked == false)){
-			//Check trait search fields if present
-			if (typeof frm.SearchByTraits !== "undefined" && frm.SearchByTraits.value == "true") {
-				var traitinputs = frm.elements;
-				var traitselected = false;
-			 	for(var i = 0; i < traitinputs.length; i++) {
-					if(traitinputs[i].name.indexOf('traitid-') == 0) {
-						if(traitinputs[i].type == 'checkbox' || traitinputs[i].type == 'radio') {
-							if(traitinputs[i].checked == true) {
-								traitselected = traitinputs[i].checked;
-								break;
-							}
-						} else {
-							if(traitinputs[i].value.trim() !== '') {
-								traitselected = true;
-								break;
-							}
-						}
-					}
-				}
-				if(!traitselected) {
-					alert("Please fill in at least one search parameter!");
-					return false;
+	let searchDefined = false;
+	let traitInputs = frm.elements;
+ 	for(var i = 0; i < traitInputs.length; i++) {
+		if(traitInputs[i].type == "text" || traitInputs[i].type == "textarea"){
+			if(traitInputs[i].value.trim() != ""){
+				searchDefined = true;
+				break;
+			}
+		}
+		else if(traitInputs[i].type == "checkbox" || traitInputs[i].type == "radio"){
+			if(traitInputs[i].name != "usethes" && traitInputs[i].name != "includeothercatnum" && traitInputs[i].name != "includecult"){
+				if(traitInputs[i].checked){
+					searchDefined = true;
+					break;
 				}
-			} else {
-				alert("Please fill in at least one search parameter!");
-				return false;
 			}
+		}
+	}
+	if(!searchDefined) {
+		alert("Please fill in at least one search parameter!");
+		return false;
 	}
 
 	if(frm.upperlat.value != '' || frm.bottomlat.value != '' || frm.leftlong.value != '' || frm.rightlong.value != ''){
@@ -62,17 +52,17 @@ function checkHarvestParamsForm(frm){
 			alert("Longitude values can not be greater than 180 or less than -180.");
 			return false;
 		}
-		var uLat = frm.upperlat.value;
+		let uLat = frm.upperlat.value;
 		if(frm.upperlat_NS.value == 'S') uLat = uLat * -1;
-		var bLat = frm.bottomlat.value;
+		let bLat = frm.bottomlat.value;
 		if(frm.bottomlat_NS.value == 'S') bLat = bLat * -1;
 		if(uLat < bLat){
 			alert("Your northern latitude value is less then your southern latitude value. Please correct this.");
 			return false;
 		}
-		var lLng = frm.leftlong.value;
+		let lLng = frm.leftlong.value;
 		if(frm.leftlong_EW.value == 'W') lLng = lLng * -1;
-		var rLng = frm.rightlong.value;
+		let rLng = frm.rightlong.value;
 		if(frm.rightlong_EW.value == 'W') rLng = rLng * -1;
 		if(lLng > rLng){
 			alert("Your western longitude value is greater then your eastern longitude value. Please correct this. Note that western hemisphere longitudes in the decimal format are negitive.");