Merge pull request #48 from bryo-lichen/master

Merging Symbiota-light developments into Bryo-lichen code repository
BioKIC · Mar 12, 2021 · cb32316 · cb32316
2 parents d9cd8c7 + bea7e64
commit cb32316
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Showing 19 changed files with 165 additions and 94 deletions.
diff --git a/checklists/dynamicmap.php b/checklists/dynamicmap.php
@@ -6,32 +6,32 @@
 $tid = array_key_exists('tid',$_REQUEST)?$_REQUEST['tid']:0;
 $taxa = array_key_exists('taxa',$_REQUEST)?$_REQUEST['taxa']:'';
 $interface = array_key_exists('interface',$_REQUEST)&&$_REQUEST['interface']?$_REQUEST['interface']:'checklist';
+$latCen = array_key_exists('lat',$_REQUEST)?$_REQUEST['lat']:'';
+$longCen = array_key_exists('long',$_REQUEST)?$_REQUEST['long']:'';
+$zoomInt = array_key_exists('zoom',$_REQUEST)?$_REQUEST['zoom']:'';
 
 //Sanitation
 if(!is_numeric($tid)) $tid = 0;
 $taxa = filter_var($taxa,FILTER_SANITIZE_STRING);
 if($interface && $interface != 'key') $interface = 'checklist';
 
 //$dynClManager = new DynamicChecklistManager();
-
-$latCen = 41.0;
-$longCen = -95.0;
-$coorArr = explode(";",$MAPPING_BOUNDARIES);
-if($coorArr && count($coorArr) == 4){
-	$latCen = ($coorArr[0] + $coorArr[2])/2;
-	$longCen = ($coorArr[1] + $coorArr[3])/2;
-}
-$coordRange = 50;
-if($coorArr && count($coorArr) == 4) $coordRange = ($coorArr[0] - $coorArr[2]);
-$zoomInt = 5;
-if($coordRange < 20){
-	$zoomInt = 6;
-}
-elseif($coordRange > 35 && $coordRange < 40){
-	$zoomInt = 4;
+if(!$latCen || !$longCen){
+	$latCen = 41.0;
+	$longCen = -95.0;
+	$coorArr = explode(";",$MAPPING_BOUNDARIES);
+	if($coorArr && count($coorArr) == 4){
+		$latCen = ($coorArr[0] + $coorArr[2])/2;
+		$longCen = ($coorArr[1] + $coorArr[3])/2;
+	}
 }
-elseif($coordRange > 40){
-	$zoomInt = 3;
+if(!$zoomInt){
+	$zoomInt = 5;
+	$coordRange = 50;
+	if($coorArr && count($coorArr) == 4) $coordRange = ($coorArr[0] - $coorArr[2]);
+	if($coordRange < 20) $zoomInt = 6;
+	elseif($coordRange > 35 && $coordRange < 40) $zoomInt = 4;
+	elseif($coordRange > 40) $zoomInt = 3;
 }
 ?>
 <html>

diff --git a/checklists/index.php b/checklists/index.php
@@ -1,9 +1,10 @@
 <?php
 include_once('../config/symbini.php');
 include_once($SERVER_ROOT.'/classes/ChecklistManager.php');
+include_once($SERVER_ROOT.'/content/lang/checklists/index.'.$LANG_TAG.'.php');
 header("Content-Type: text/html; charset=".$CHARSET);
 
-$pid = array_key_exists("pid",$_REQUEST)?$_REQUEST["pid"]:0;
+$pid = array_key_exists('pid',$_REQUEST)?$_REQUEST['pid']:0;
 
 $clManager = new ChecklistManager();
 $clManager->setProj($pid);
@@ -21,57 +22,52 @@
 		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" />';
 	}
+	include_once($SERVER_ROOT.'/includes/googleanalytics.php');
 	?>
-	<script type="text/javascript">
-		<?php include_once($SERVER_ROOT.'/includes/googleanalytics.php'); ?>
-	</script>
 </head>
 <body>
 	<?php
-	$displayLeftMenu = (isset($checklists_indexMenu)?$checklists_indexMenu:"true");
-	include($SERVER_ROOT."/includes/header.php");
-	echo "<div class='navpath'>";
-	echo "<a href='../index.php'>Home</a> &gt;&gt; ";
-	if(isset($checklists_indexCrumbs) && $checklists_indexCrumbs) echo $checklists_indexCrumbs.' &gt;&gt;';
-	echo " <b>Species Checklists</b>";
-	echo "</div>";
+	$displayLeftMenu = (isset($checklists_indexMenu)?$checklists_indexMenu:'true');
+	include($SERVER_ROOT.'/includes/header.php');
 	?>
-	<!-- This is inner text! -->
+	<div class="navpath">
+		<a href="../index.php"><?php echo (isset($LANG['NAV_HOME'])?$LANG['NAV_HOME']:'Home'); ?></a> &gt;&gt;
+		<b><?php echo (isset($LANG['SPECIES_INVENTORIES'])?$LANG['SPECIES_INVENTORIES']:'Species Inventories'); ?></b>
+	</div>
 	<div id="innertext">
-		<h1>Species Checklists</h1>
-        <div style='margin:20px;'>
+		<h1><?php echo (isset($LANG['SPECIES_INVENTORIES'])?$LANG['SPECIES_INVENTORIES']:'Species Inventories'); ?></h1>
+        <div style="margin:20px;">
 			<?php
             $researchArr = $clManager->getChecklists();
 			if($researchArr){
 				foreach($researchArr as $pid => $projArr){
 					?>
-					<div style='margin:3px 0px 0px 15px;'>
-						<h3><?php echo $projArr['name']; ?>
-							<a href="<?php echo "clgmap.php?pid=".$pid; ?>" title='Show checklists on map'>
-								<img src='../images/world.png' style='width:10px;border:0' />
-							</a>
-						</h3>
-						<div>
-							<ul>
-								<?php
-								foreach($projArr['clid'] as $clid => $clName){
-									echo "<li><a href='checklist.php?clid=".$clid."&pid=".$pid."'>".$clName."</a></li>\n";
-								}
-								?>
-							</ul>
-						</div>
-					</div>
+					<h3>
+						<?php
+						$projName = $projArr['name'];
+						if($projName == 'Miscellaneous Inventories') $projName = (isset($LANG['MISC_INVENTORIES'])?$LANG['MISC_INVENTORIES']:'Miscellaneous Inventories');
+						echo $projName;
+						?>
+						<a href="<?php echo "clgmap.php?pid=".$pid; ?>" title='<?php echo (isset($LANG['SHOW_MAP'])?$LANG['SHOW_MAP']:'Show inventories on map'); ?>'>
+							<img src='../images/world.png' style='width:10px;border:0' />
+						</a>
+					</h3>
+					<ul>
+						<?php
+						foreach($projArr['clid'] as $clid => $clName){
+							echo '<li><a href="checklist.php?clid='.$clid.'&pid='.$pid.'">'.$clName.'</a></li>';
+						}
+						?>
+					</ul>
 					<?php
 				}
 			}
-			else{
-				echo '<div><b>No Checklists returned</b></div>';
-			}
+			else echo '<div><b>'.(isset($LANG['NO_INVENTORIES'])?$LANG['NO_INVENTORIES']:'No inventories returned').'</b></div>';
 			?>
 		</div>
 	</div>
 	<?php
-		include($SERVER_ROOT."/includes/footer.php");
+	include($SERVER_ROOT.'/includes/footer.php');
 	?>
 </body>
 </html>
diff --git a/classes/DwcArchiverCore.php b/classes/DwcArchiverCore.php
@@ -1662,7 +1662,8 @@ private function writeOccurrenceFile(){
 				elseif($this->schemaType == 'backup') unset($r['collid']);
 
 				if($ocnStr = $dwcOccurManager->getAdditionalCatalogNumberStr($r['occid'])) $r['otherCatalogNumbers'] = $ocnStr;
-				if($assocStr = $dwcOccurManager->getAssociationStr($r['occid'])) $r['t_associatedOccurrences'] = $assocStr;
+				if($assocOccurStr = $dwcOccurManager->getAssociationStr($r['occid'])) $r['t_associatedOccurrences'] = $assocOccurStr;
+				if($assocTaxa = $dwcOccurManager->getAssocTaxa($r['occid'])) $r['associatedTaxa'] = $assocTaxa;
 				//$dwcOccurManager->appendUpperTaxonomy($r);
 				$dwcOccurManager->appendUpperTaxonomy2($r);
 				if($rankStr = $dwcOccurManager->getTaxonRank($r['rankid'])) $r['t_taxonRank'] = $rankStr;

diff --git a/classes/DwcArchiverOccurrence.php b/classes/DwcArchiverOccurrence.php
@@ -409,6 +409,21 @@ public function getAssociationStr($occid){
 		return trim($retStr,' |');
 	}
 
+	public function getAssocTaxa($occid){
+		$retStr = '';
+		if($occid){
+			$sql = 'SELECT assocID, relationship, subType, verbatimSciname FROM omoccurassociations WHERE occid = '.$occid.' AND verbatimSciname IS NOT NULL ';
+			$rs = $this->conn->query($sql);
+			if($rs){
+				while($r = $rs->fetch_object()){
+					$retStr .= '|'.$r->relationship.($r->subType?' ('.$r->subType.')':'').': '.$r->verbatimSciname;
+				}
+				$rs->free();
+			}
+		}
+		return trim($retStr,' |');
+	}
+
 	private function getInverseRelationship($relationship){
 		if(!$this->relationshipArr) $this->setRelationshipArr();
 		if(array_key_exists($relationship, $this->relationshipArr)) return $this->relationshipArr[$relationship];

diff --git a/classes/ImageCleaner.php b/classes/ImageCleaner.php
@@ -105,11 +105,12 @@ public function buildThumbnailImages(){
 
 	private function setCollectionCode(){
 		if($this->collid && !$this->collMetaArr){
-			$sql = 'SELECT collid, CONCAT_WS("_",institutioncode, collectioncode) AS code, collectionname FROM omcollections WHERE collid = '.$this->collid;
+			$sql = 'SELECT collid, CONCAT_WS("_",institutioncode, collectioncode) AS code, collectionname, managementType FROM omcollections WHERE collid = '.$this->collid;
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
 				$this->collMetaArr[$r->collid]['code'] = $r->code;
 				$this->collMetaArr[$r->collid]['name'] = $r->collectionname;
+				$this->collMetaArr[$r->collid]['managementType'] = $r->managementType;
 			}
 			$rs->free();
 		}
@@ -278,9 +279,8 @@ private function getTropicosWebUrl2($url){
 			$imageID = $m[1];
 			$imgDisplayUrl = 'http://www.tropicos.org/Image/'.$imageID;
 			$ip = $_SERVER['HTTP_HOST'];
-
-			$header[0]  = "Accept: text/xml,application/xml,application/xhtml+xml,";
-			$header[0] .= "text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5";
+			$header = array();
+			$header[]  = "Accept: text/xml,application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5";
 			$header[] = "Cache-Control: max-age=0";
 			$header[] = "Connection: keep-alive";
 			$header[] = "Keep-Alive: 300";
@@ -520,7 +520,7 @@ public function recycleImagesFromFile($filePath){
 		$this->setRecycleBin();
 		if(!$filePath) exit('Image identifier file path IS NULL');
 		if(!file_exists($filePath)) exit('Image identifier file Not Found');
-		if(($imgidHandler = fopen($imgidFile, 'r')) !== FALSE){
+		if(($imgidHandler = fopen($filePath, 'r')) !== FALSE){
 			while(($data = fgets($imgidHandler)) !== FALSE){
 				$this->recycleImage($data[0]);
 			}
@@ -660,6 +660,15 @@ public function getCollectionName(){
 		return $retStr;
 	}
 
+	public function getManagementType(){
+		$retStr = '';
+		if($this->collid){
+			if(!$this->collMetaArr) $this->setCollectionCode();
+			$retStr = $this->collMetaArr[$this->collid]['managementType'];
+		}
+		return $retStr;
+	}
+
 	public function setBuildMediumDerivative($bool){
 		if($bool) $this->buildMediumDerivative = true;
 		else $this->buildMediumDerivative = false;

diff --git a/classes/ImageShared.php b/classes/ImageShared.php
@@ -401,14 +401,13 @@ public function processImage(){
 		if(!$this->imgWebUrl && $this->createWebDerivative){
 			if($this->sourceWidth < ($this->webPixWidth*1.2) && $this->sourceFileSize < $this->webFileSizeLimit){
 				//Source image width and file size is small enough to serve as web image
-				if(strtolower(substr($this->sourcePath,0,7)) == 'http://' || strtolower(substr($this->sourcePath,0,8)) == 'https://'){
+				if(strtolower(substr($this->sourcePath,0,4)) == 'http'){
 					if(copy($this->sourcePath, $this->targetPath.$this->imgName.$this->imgExt, $this->context)){
 						$this->imgWebUrl = $this->imgName.$this->imgExt;
 					}
 				}
-				else{
-					$this->imgWebUrl = $this->imgName.$this->imgExt;
-				}
+				elseif($this->imgLgUrl) $this->imgWebUrl = $this->imgLgUrl;
+				else $this->imgWebUrl = basename($this->sourcePath);
 			}
 			else{
 				//Image width or file size is too large
@@ -910,6 +909,10 @@ public function setSourceUrl($v){
 		$this->sourceUrl = $this->cleanInStr($v);
 	}
 
+	public function setImgLgUrl($v){
+		$this->imgLgUrl = $this->cleanInStr($v);
+	}
+
 	public function setImgWebUrl($v){
 		$this->imgWebUrl = $this->cleanInStr($v);
 	}

diff --git a/classes/OccurrenceEditorImages.php b/classes/OccurrenceEditorImages.php
@@ -291,12 +291,11 @@ public function addImage($postArr){
 			if(array_key_exists('copytoserver',$postArr) && $postArr['copytoserver']){
 				if(!$imgManager->copyImageFromUrl()) $status = false;
 			}
+			else $imgManager->setImgLgUrl($sourceImgUri);
 		}
 		else{
 			//Image is a file upload
-			if(!$imgManager->uploadImage()){
-				$status = false;
-			}
+			if(!$imgManager->uploadImage()) $status = false;
 		}
 		$imgManager->setOccid($this->occid);
 		if(isset($this->occurrenceMap[$this->occid]['tidinterpreted'])) $imgManager->setTid($this->occurrenceMap[$this->occid]['tidinterpreted']);

diff --git a/classes/OccurrenceSesar.php b/classes/OccurrenceSesar.php
@@ -56,7 +56,7 @@ public function getSesarProfile(){
 	}
 
 	private function setDynamicPropertiesArr(){
-		if($this->dynPropArr === false){
+		if($this->dynPropArr === false && $this->collid){
 			$this->dynPropArr = array();
 			$sql = 'SELECT dynamicProperties FROM omcollections WHERE collid = '.$this->collid;
 			$rs = $this->conn->query($sql);
@@ -619,6 +619,10 @@ private function setMissingSesarMeta(&$sesarResultArr){
 					$catNum = $m[1];
 					$occid = $m[2];
 					$sesarResultArr['missing'][$lostIGSN] = array('catNum'=>$catNum,'occid'=>$occid);
+					$sql1 = 'UPDATE igsnverification SET occid = '.$occid.' WHERE igsn = "'.$lostIGSN.'"';
+					$this->conn->query($sql1);
+					$sql2 = 'UPDATE igsnverification SET catalogNumber = "'.$catNum.'" WHERE igsn = "'.$lostIGSN.'"';
+					$this->conn->query($sql2);
 				}
 			}
 			$cnt++;
@@ -644,17 +648,19 @@ public function syncIGSN($occid,$catalogNumber,$igsn){
 		$ok = true;
 		$retArr = array('status'=>0);
 		if(is_numeric($occid) && preg_match('/^[A-Z0-9]+$/', $igsn)){
-			$sql = 'SELECT catalogNumber, occurrenceID FROM omoccurrences WHERE occid = '.$occid;
+			$sql = 'SELECT catalogNumber, otherCatalogNumbers, occurrenceID FROM omoccurrences WHERE occid = '.$occid;
 			$rs = $this->conn->query($sql);
 			if($r = $rs->fetch_object()){
 				if($r->occurrenceID){
 					$retArr['errCode'] = 1;
 					$retArr['guid'] = $r->occurrenceID;
 					$ok = false;
 				}
-				elseif($r->catalogNumber != $catalogNumber){
+				elseif($r->catalogNumber != $catalogNumber && $r->otherCatalogNumbers != $catalogNumber){
 					$retArr['errCode'] = 2;
-					$retArr['catNum'] = $r->catalogNumber;
+					$catNum = $r->catalogNumber;
+					if($r->otherCatalogNumbers) $catNum .= ', '.$r->otherCatalogNumbers;
+					$retArr['catNum'] = trim($catNum,', ');
 					$ok = false;
 				}
 			}

diff --git a/collections/admin/igsnmanagement.php b/collections/admin/igsnmanagement.php
@@ -196,7 +196,7 @@ function verifyProfileForm(f){
 				if($missingCnt){
 					echo '<div id="missingGuidList" style="margin-left:40px;display:none">';
 					foreach($sesarArr['missing'] as $igsn => $missingArr){
-						echo '<li><a href="https://sesardev.geosamples.org/sample/igsn/'.$igsn.'" target="_blank" title="Open IGSN in SESAR Systems">'.$igsn.'</a> ';
+						echo '<li><a href="https://app.geosamples.org/sample/igsn/'.$igsn.'" target="_blank" title="Open IGSN in SESAR Systems">'.$igsn.'</a> ';
 						if(isset($missingArr['occid'])){
 							echo '=> <a href="../editor/occurrenceeditor.php?occid='.$missingArr['occid'].'" target="_blank" title="Open occurrence in editor">'.$missingArr['catNum'].'</a> ';
 							echo '<a href="#" onclick="syncIGSN('.$missingArr['occid'].',\''.$missingArr['catNum'].'\',\''.$igsn.'\');return false" title="Add IGSN to target occurrence"><img src="../../images/link.png" style="width:13px"/></a>';

diff --git a/collections/individual/index.php b/collections/individual/index.php
@@ -865,8 +865,13 @@ function initializeMap(){
 								<?php
 								foreach($iArr as $imgId => $imgArr){
 									$thumbUrl = $imgArr['tnurl'];
-									if(!$thumbUrl || substr($thumbUrl,0,7)=='process') $thumbUrl = $imgArr['url'];
-									if(!$thumbUrl || substr($thumbUrl,0,7)=='process') $thumbUrl = $imgArr['lgurl'];
+									if(!$thumbUrl || substr($thumbUrl,0,7)=='process'){
+										if($image = exif_thumbnail($imgArr['lgurl'])){
+											$thumbUrl = 'data:image/jpeg;base64,'.base64_encode($image);
+										}
+										elseif($imgArr['url'] && substr($imgArr['url'],0,7)!='process') $thumbUrl = $imgArr['url'];
+										else $thumbUrl = $imgArr['lgurl'];
+									}
 									?>
 									<div class="imgDiv">
 										<a href='<?php echo $imgArr['url']; ?>' target="_blank">

diff --git a/config/schema-1.0/dev/db_schema_patch_pending.sql b/config/schema-1.0/dev/db_schema_patch_pending.sql
@@ -447,6 +447,8 @@ CREATE TABLE `igsnverification` (
   INDEX `INDEX_igsn` (`igsn` ASC),
   CONSTRAINT `FK_igsn_occid`  FOREIGN KEY (`occid`)  REFERENCES `omoccurrences` (`occid`)  ON DELETE CASCADE  ON UPDATE CASCADE);
 
+ALTER TABLE `igsnverification` 
+ ADD COLUMN `catalogNumber` VARCHAR(45) NULL AFTER `occid`;
 
 CREATE TABLE `omoccurloanuser` (
   `loanid` INT UNSIGNED NOT NULL,

diff --git a/content/lang/checklists/index.en.php b/content/lang/checklists/index.en.php
@@ -0,0 +1,13 @@
+<?php
+/*
+------------------
+Language: English
+------------------
+*/
+
+$LANG['NAV_HOME'] = 'Home';
+$LANG['SPECIES_INVENTORIES'] = 'Species Inventories';
+$LANG['SHOW_MAP'] = 'Show inventories on map';
+$LANG['NO_INVENTORIES'] = 'No inventories returned';
+$LANG['MISC_INVENTORIES'] = 'Miscellaneous Inventories';
+?>
diff --git a/content/lang/checklists/index.es.php b/content/lang/checklists/index.es.php
@@ -0,0 +1,13 @@
+<?php
+/*
+------------------
+Language: Español (Spanish)
+------------------
+*/
+
+$LANG['NAV_HOME'] = 'Inicio';
+$LANG['SPECIES_INVENTORIES'] = 'Inventarios de Especies';
+$LANG['SHOW_MAP'] = 'Mostrar inventarios en el mapa';
+$LANG['NO_INVENTORIES'] = 'Sin inventories';
+$LANG['MISC_INVENTORIES'] = 'Inventarios Varios';
+?>
diff --git a/content/lang/sitemap.en.php b/content/lang/sitemap.en.php
@@ -26,7 +26,8 @@
 $LANG['GLOSSARY'] = 'Glossary';
 $LANG['PROTECTED_SPECIES'] = 'Protected Species';
 $LANG['LISTOFTAXA'] = 'list of taxa where locality and/or taxonomic information is protected due to rare/threatened/endangered status';
-$LANG['BIOINV'] = 'Biotic Inventory Projects';
+$LANG['BIOTIC_INVENTORIES'] = 'Biotic Inventory Projects';
+$LANG['ALL_CHECKLISTS'] = 'All Public Checklists';
 $LANG['DYNAMIC'] = 'Dynamic Species Lists';
 $LANG['CHECKLIST'] = 'Checklist';
 $LANG['BUILDCHECK'] = 'dynamically build a checklist using georeferenced specimen records';