Merge pull request #52 from BioKIC/master

Merge BioKIC/Symbiota-light developments into CCH2 code repository

README.md

@@ -7,7 +7,7 @@ something far greater than a single entity is capable of doing on their own.
 
 More information about this project can be accessed through:
 
-(http://symbiota.org)
+(https://symbiota.org)
 
 
 ## ACKNOWLEDGEMENTS

agents/index.php

@@ -97,7 +97,6 @@ function pageheader($name) {
 	<meta name="keywords" content='. $spDisplay .' />
 	<link href="../css/base.css?ver=<?php echo $CSS_VERSION; ?>" type="text/css" rel="stylesheet" />
 	<link href="../css/main.css'.(isset($CSS_VERSION_LOCAL)?'?ver='.$CSS_VERSION_LOCAL:'').'" type="text/css" rel="stylesheet" />
-	<link href="../css/speciesprofilebase.css" type="text/css" rel="stylesheet" />
 	<script type="text/javascript" src="../js/jquery.js"></script>
 	<script type="text/javascript" src="../js/jquery-ui.js"></script>';
     // include_once($SERVER_ROOT.'/includes/googleanalytics.php');

classes/DwcArchiverCore.php

@@ -1524,7 +1524,8 @@ private function writeOccurrenceFile(){
 		$dwcOccurManager = new DwcArchiverOccurrence($this->conn);
 		$dwcOccurManager->setSchemaType($this->schemaType);
 		$dwcOccurManager->setExtended($this->extended);
-		$dwcOccurManager->setHarvestExsiccatae();
+		$dwcOccurManager->setIncludeExsiccatae();
+		$dwcOccurManager->setIncludeAssociatedSequences();
 		$dwcOccurManager->setIncludePaleo($this->hasPaleo);
 		if(!$this->occurrenceFieldArr) $this->occurrenceFieldArr = $dwcOccurManager->getOccurrenceArr($this->schemaType, $this->extended);
 		//Output records
@@ -1668,6 +1669,7 @@ private function writeOccurrenceFile(){
 					$r['occurrenceRemarks'] = $exsStr;
 				}
 				if($assocOccurStr = $dwcOccurManager->getAssociationStr($r['occid'])) $r['t_associatedOccurrences'] = $assocOccurStr;
+				if($assocSeqStr = $dwcOccurManager->getAssociatedSequencesStr($r['occid'])) $r['t_associatedSequences'] = $assocSeqStr;
 				if($assocTaxa = $dwcOccurManager->getAssocTaxa($r['occid'])) $r['associatedTaxa'] = $assocTaxa;
 				//$dwcOccurManager->appendUpperTaxonomy($r);
 				$dwcOccurManager->appendUpperTaxonomy2($r);

classes/DwcArchiverOccurrence.php

@@ -6,7 +6,8 @@ class DwcArchiverOccurrence{
 	private $schemaType;
 	private $extended = false;
 	private $includePaleo = false;
-	private $harvestExsiccatae = false;
+	private $includeExsiccatae = false;
+	private $includeAssocSeq = false;
 	private $relationshipArr;
 	private $upperTaxonomy = array();
 	private $taxonRankArr = array();
@@ -124,6 +125,8 @@ public function getOccurrenceArr(){
 		$this->occurDefArr['fields']['dynamicProperties'] = 'o.dynamicProperties';
 		$this->occurDefArr['terms']['associatedOccurrences'] = 'http://rs.tdwg.org/dwc/terms/associatedOccurrences';
 		$this->occurDefArr['fields']['associatedOccurrences'] = '';
+		$this->occurDefArr['terms']['associatedSequences'] = 'http://rs.tdwg.org/dwc/terms/associatedSequences';
+		$this->occurDefArr['fields']['associatedSequences'] = '';
 		$this->occurDefArr['terms']['associatedTaxa'] = 'http://rs.tdwg.org/dwc/terms/associatedTaxa';
 		$this->occurDefArr['fields']['associatedTaxa'] = 'o.associatedTaxa';
 		$this->occurDefArr['terms']['reproductiveCondition'] = 'http://rs.tdwg.org/dwc/terms/reproductiveCondition';
@@ -348,7 +351,7 @@ public function getSqlOccurrences($fieldArr, $fullSql = true){
 	//Special functions for appending additional data
 	public function getAdditionalCatalogNumberStr($occid){
 		$retStr = '';
-		if($occid){
+		if(is_numeric($occid)){
 			$sql = 'SELECT GROUP_CONCAT(CONCAT_WS(": ",identifierName, identifierValue) SEPARATOR "; ") as idStr FROM omoccuridentifiers WHERE occid = '.$occid;
 			$rs = $this->conn->query($sql);
 			if($r = $rs->fetch_object()){
@@ -359,35 +362,37 @@ public function getAdditionalCatalogNumberStr($occid){
 		return $retStr;
 	}
 
-	public function setHarvestExsiccatae(){
+	public function setIncludeExsiccatae(){
 		$sql = 'SELECT occid FROM omexsiccatiocclink LIMIT 1';
 		$rs = $this->conn->query($sql);
-		if($rs->num_rows) $this->harvestExsiccatae = true;
+		if($rs->num_rows) $this->includeExsiccatae = true;
 		$rs->free();
 	}
 
 	public function getExsiccateStr($occid){
 		$retStr = '';
-		$sql = 'SELECT t.title, t.abbreviation, t.editor, t.exsrange, n.exsnumber, l.notes '.
-			'FROM omexsiccatiocclink l INNER JOIN omexsiccatinumbers n ON l.omenid = n.omenid '.
-			'INNER JOIN omexsiccatititles t ON n.ometid = t.ometid '.
-			'WHERE l.occid = '.$occid;
-		$rs = $this->conn->query($sql);
-		while($r = $rs->fetch_object()){
-			$retStr = $r->title;
-			if($r->abbreviation) $retStr .= ' ['.$r->abbreviation.']';
-			if($r->exsrange) $retStr .= ', '.$r->exsrange;
-			if($r->editor) $retStr .= ', '.$r->editor;
-			$retStr .= ', exs #: '.$r->exsnumber;
-			if($r->notes) $retStr .= ' ('.$r->notes.')';
+		if($this->includeExsiccatae && is_numeric($occid)){
+			$sql = 'SELECT t.title, t.abbreviation, t.editor, t.exsrange, n.exsnumber, l.notes '.
+				'FROM omexsiccatiocclink l INNER JOIN omexsiccatinumbers n ON l.omenid = n.omenid '.
+				'INNER JOIN omexsiccatititles t ON n.ometid = t.ometid '.
+				'WHERE l.occid = '.$occid;
+			$rs = $this->conn->query($sql);
+			while($r = $rs->fetch_object()){
+				$retStr = $r->title;
+				if($r->abbreviation) $retStr .= ' ['.$r->abbreviation.']';
+				if($r->exsrange) $retStr .= ', '.$r->exsrange;
+				if($r->editor) $retStr .= ', '.$r->editor;
+				$retStr .= ', exs #: '.$r->exsnumber;
+				if($r->notes) $retStr .= ' ('.$r->notes.')';
+			}
+			$rs->free();
 		}
-		$rs->free();
 		return $retStr;
 	}
 
 	public function getAssociationStr($occid){
 		$retStr = '';
-		if($occid){
+		if(is_numeric($occid)){
 			$sql = 'SELECT assocID, occid, occidAssociate, relationship, subType, resourceUrl, identifier FROM omoccurassociations WHERE (occid = '.$occid.' OR occidAssociate = '.$occid.') AND verbatimSciname IS NULL ';
 			$rs = $this->conn->query($sql);
 			if($rs){
@@ -436,9 +441,35 @@ public function getAssociationStr($occid){
 		return trim($retStr,' |');
 	}
 
+	public function setIncludeAssociatedSequences(){
+		$sql = 'SELECT occid FROM omoccurgenetic LIMIT 1';
+		$rs = $this->conn->query($sql);
+		if($rs->num_rows) $this->includeAssocSeq = true;
+		$rs->free();
+	}
+
+	public function getAssociatedSequencesStr($occid){
+		$retStr = '';
+		if(is_numeric($occid)){
+			$sql = 'SELECT identifier, resourceName, title, locus, resourceUrl FROM omoccurgenetic WHERE occid = '.$occid;
+			$rs = $this->conn->query($sql);
+			if($rs){
+				while($r = $rs->fetch_object()){
+					$retStr .= '|'.$r->resourceName.', ';
+					if($r->title) $retStr .= $r->title.', ';
+					if($r->identifier) $retStr .= $r->identifier.', ';
+					if($r->locus) $retStr .= $r->locus.', ';
+					$retStr .= $r->resourceUrl;
+				}
+				$rs->free();
+			}
+		}
+		return trim($retStr,' |,');
+	}
+
 	public function getAssocTaxa($occid){
 		$retStr = '';
-		if($occid){
+		if(is_numeric($occid)){
 			$sql = 'SELECT assocID, relationship, subType, verbatimSciname FROM omoccurassociations WHERE occid = '.$occid.' AND verbatimSciname IS NOT NULL ';
 			$rs = $this->conn->query($sql);
 			if($rs){

classes/GlossaryManager.php

@@ -1364,7 +1364,6 @@ public function getTaxaList($queryString, $type){
 				'WHERE (t.SciName LIKE "'.$queryString.'%" OR v.VernacularName LIKE "'.$queryString.'%") AND t.RankId < 185 AND ts.taxauthid = 1 '.
 				'ORDER BY t.SciName, v.sortsequence LIMIT 20 ';
 			$rs = $this->conn->query($sql);
-			$taxa = array();
 			if($type == 'single'){
 				while ($row = $rs->fetch_object()) {
 					$sciName = $row->SciName;

classes/GlossaryUpload.php

@@ -59,7 +59,6 @@ public function loadFile($fieldMap,$languageArr,$tidStr,$batchSources){
 		$this->conn->query("TRUNCATE TABLE uploadglossary");
 		$this->conn->query("OPTIMIZE TABLE uploadglossary");
 		$fh = fopen($this->uploadTargetPath.$this->uploadFileName,'r') or die("Can't open file");
-		$headerArr = fgetcsv($fh);
 		$newTermColumn = false;
 		foreach($languageArr as $lang){
 			foreach($fieldMap as $csvField => $field){
@@ -200,7 +199,6 @@ public function cleanUpload($tidStr){
 	}
 
 	public function analysisUpload(){
-		$retArr = array();
 		//Get total number
 		$sql1 = 'SELECT count(*) as cnt FROM uploadglossary';
 		$rs1 = $this->conn->query($sql1);

classes/OccurrenceDuplicate.php

@@ -48,7 +48,7 @@ public function getClusterArr($occid){
 			if($rs = $this->conn->query($sql)){
 				while($r = $rs->fetch_object()){
 					$retArr[$r->duplicateid]['o'][$r->occid] = array('instcode' => $r->institutioncode, 'collcode' => $r->collectioncode,
-							'collname' => $r->collectionname, 'catnum' => $r->catalognumber, 'occurrenceid' => $r->occurrenceid, 'sciname' => $r->sciname, 'author' => $r->scientificnameauthorship,
+					'collname' => $r->collectionname, 'catnum' => $r->catalognumber, 'occurrenceid' => $r->occurrenceid, 'sciname' => $r->sciname, 'author' => $r->scientificnameauthorship,
 					'identifiedby' => $r->identifiedby, 'dateidentified' => $r->dateidentified, 'recordedby' => $r->recordedby,
 					'recordnumber' => $r->recordnumber, 'eventdate' => $r->eventdate, 'notes' => $r->notes, 'tnurl' => $r->thumbnailurl,
 					'url' => $r->url);

classes/OccurrenceEditReview.php

@@ -1,5 +1,4 @@
 <?php
-include_once($SERVER_ROOT.'/config/dbconnection.php');
 include_once($SERVER_ROOT.'/classes/Manager.php');
 
 class OccurrenceEditReview extends Manager{

classes/OccurrenceEditorManager.php

@@ -657,8 +657,6 @@ protected function setOccurArr($start = 0, $limit = 0){
 		}
 		if($sqlFrag){
 			$sql = 'SELECT DISTINCT o.occid, o.collid, o.'.implode(',o.',$this->occFieldArr).' FROM omoccurrences o '.$sqlFrag;
-			//$sql = 'SELECT o.occid, o.collid, o.'.implode(',o.',$this->occFieldArr).' FROM omoccurrences o '.$sqlFrag;
-			//echo "<div>".$sql."</div>";
 			$previousOccid = 0;
 			$rs = $this->conn->query($sql);
 			$rsCnt = 0;
@@ -672,7 +670,7 @@ protected function setOccurArr($start = 0, $limit = 0){
 					elseif($this->occid == $row['occid']){
 						//Is target specimen
 						$retArr[$row['occid']] = array_change_key_case($row);
-						if($this->collMap['colltype'] == 'General Observations' && $row->observeruid == $GLOBALS['SYMB_UID']) $this->isPersonalManagement = true;
+						if($this->collMap['colltype'] == 'General Observations' && $row['observeruid'] == $GLOBALS['SYMB_UID']) $this->isPersonalManagement = true;
 					}
 					elseif(is_numeric($localIndex) && $localIndex == $rsCnt){
 						$retArr[$row['occid']] = array_change_key_case($row);

classes/OccurrenceEditorMaterialSample.php

@@ -0,0 +1,35 @@
+<?php
+include_once($SERVER_ROOT.'/classes/Manager.php');
+
+class OccurrenceEditorMaterialSample extends Manager{
+
+	private $occid;
+
+	function __construct(){
+		parent::__construct(null,'write');
+	}
+
+	function __destruct(){
+ 		parent::__destruct();
+	}
+
+	public function getMaterialSampleArr(){
+		$retArr = array();
+		$sql = 'SELECT msID, materialSampleType, concentration, concentrationUnit, concentrationMethod, ratioOfAbsorbance260_230, ratioOfAbsorbance260_280, volume, volumeUnit, '.
+			'weight, weightUnit, weightMethod, purificationMethod, quality, qualityRemarks, qualityCheckDate, sampleSize, sieving, dnaHybridization, dnaMeltingPoint, '.
+			'estimatedSize, poolDnaExtracts, sampleDesignation, initialTimestamp '.
+			'FROM ommaterialsample '.
+			'WHERE occid = '.$this->occid;
+		$rs = $this->conn->query($sql);
+		while($r = $rs->fetch_assoc()){
+			$retArr[$r['msID']] = $r;
+		}
+		$rs->free();
+		return $retArr;
+	}
+
+	public function setOccid($id){
+		if(is_numeric($id)) $this->occid = $id;
+	}
+}
+?>

classes/OccurrenceIndividual.php

@@ -1,6 +1,5 @@
 <?php
 include_once('Manager.php');
-include_once('OccurrenceDuplicate.php');
 include_once('OccurrenceAccessStats.php');
 
 class OccurrenceIndividual extends Manager{
@@ -357,9 +356,35 @@ private function setReferences(){
 	}
 
 	public function getDuplicateArr(){
-		$dupManager = new OccurrenceDuplicate();
-		$retArr = $dupManager->getClusterArr($this->occid);
-		unset($retArr[$this->occid]);
+		$retArr = array();
+		$sqlBase = 'SELECT o.occid, c.institutioncode AS instcode, c.collectioncode AS collcode, c.collectionname AS collname, o.catalognumber, o.occurrenceid, o.sciname, '.
+			'o.scientificnameauthorship AS author, o.identifiedby, o.dateidentified, o.recordedby, o.recordnumber, o.eventdate, IFNULL(i.thumbnailurl, i.url) AS url ';
+		//Get exsiccati duplicates
+		if(isset($this->occArr['exs'])){
+			$sql = $sqlBase.'FROM omexsiccatiocclink l INNER JOIN omexsiccatiocclink l2 ON l.omenid = l2.omenid '.
+				'INNER JOIN omoccurrences o ON l2.occid = o.occid '.
+				'INNER JOIN omcollections c ON o.collid = c.collid '.
+				'LEFT JOIN images i ON o.occid = i.occid '.
+				'WHERE l.occid = '.$this->occid;
+			if($rs = $this->conn->query($sql)){
+				while($r = $rs->fetch_assoc()){
+					$retArr['exs'][$r['occid']] = array_change_key_case($r);
+				}
+				$rs->free();
+			}
+		}
+		//Get specimen duplicates
+		$sql = $sqlBase.'FROM omoccurduplicatelink d INNER JOIN omoccurduplicatelink d2 ON d.duplicateid = d2.duplicateid '.
+			'INNER JOIN omoccurrences o ON d2.occid = o.occid '.
+			'INNER JOIN omcollections c ON o.collid = c.collid '.
+			'LEFT JOIN images i ON o.occid = i.occid '.
+			'WHERE (d.occid = '.$this->occid.') AND (d.occid != d2.occid) ';
+		if($rs = $this->conn->query($sql)){
+			while($r = $rs->fetch_assoc()){
+				if(!isset($retArr['exs'][$r['occid']])) $retArr['dupe'][$r['occid']] = array_change_key_case($r);
+			}
+			$rs->free();
+		}
 		return $retArr;
 	}
 

classes/OccurrenceLoans.php

@@ -592,11 +592,10 @@ public function editSpecimen($reqArr){
 		$status = false;
 		if(!array_key_exists('occid',$reqArr)) return;
 		$occidArr = $reqArr['occid'];
-		$applyTask = $reqArr['applytask'];
 		$loanid = $reqArr['loanid'];
 		if(is_numeric($loanid)){
 			if($occidArr){
-				if($applyTask == 'delete'){
+				if($reqArr['applytask'] == 'delete'){
 					$sql = 'DELETE FROM omoccurloanslink WHERE loanid = '.$loanid.' AND (occid IN('.implode(',',$occidArr).')) ';
 					if($this->conn->query($sql)) $status = true;
 					else $this->errorMessage = 'ERROR removing specimen from loan: '.$this->conn->error;
@@ -611,24 +610,27 @@ public function editSpecimen($reqArr){
 		return $status;
 	}
 
-	public function getSpecimenNotes($loanId, $occid){
-		$noteStr = '';
+	public function getSpecimenDetails($loanId, $occid){
+		$retArr = array();
 		if(is_numeric($loanId) && is_numeric($occid)){
-			$sql = 'SELECT notes FROM omoccurloanslink WHERE loanid = '.$loanId.' AND occid = '.$occid;
+			$sql = 'SELECT DATE_FORMAT(returndate, "%Y-%m-%dT%H:%i") AS returndate, notes FROM omoccurloanslink WHERE loanid = '.$loanId.' AND occid = '.$occid;
 			if($rs = $this->conn->query($sql)){
 				while($r = $rs->fetch_object()){
-					$noteStr = $r->notes;
+					$retArr['returnDate'] = $r->returndate;
+					$retArr['notes'] = $r->notes;
 				}
 				$rs->free();
 			}
 		}
-		return $noteStr;
+		return $retArr;
 	}
 
-	public function editSpecimenNotes($loanId, $occid, $noteStr){
+	public function editSpecimenDetails($loanId, $occid, $returnDate, $noteStr){
 		$status = false;
 		if(is_numeric($loanId) && is_numeric($occid)){
-			$sql = 'UPDATE omoccurloanslink SET notes = '.($noteStr?'"'.$this->cleanInStr($noteStr).'"':'NULL').' WHERE (loanid = '.$loanId.') AND (occid = '.$occid.')';
+			$sql = 'UPDATE omoccurloanslink '.
+				'SET returnDate = '.($returnDate?'"'.$this->cleanInStr($returnDate).'"':'NULL').', notes = '.($noteStr?'"'.$this->cleanInStr($noteStr).'"':'NULL').' '.
+				'WHERE (loanid = '.$loanId.') AND (occid = '.$occid.')';
 			if($this->conn->query($sql)) $status = true;
 			else $this->errorMessage = 'ERROR updating specimen notes: '.$this->conn->error;
 		}

classes/OccurrenceMaintenance.php

@@ -378,14 +378,16 @@ public function updateCollectionStats($collid, $full = false){
 			$rs->free();
 
 			if($this->verbose) $this->outputMsg('Calculating genetic resources counts... ',1);
-			$sql = 'SELECT COUNT(CASE WHEN g.resourceurl LIKE "http://www.boldsystems%" THEN o.occid ELSE NULL END) AS boldcnt, '.
-				'COUNT(CASE WHEN g.resourceurl LIKE "http://www.ncbi%" THEN o.occid ELSE NULL END) AS gencnt '.
+			$sql = 'SELECT COUNT(CASE WHEN g.resourceurl LIKE "%boldsystems%" THEN o.occid ELSE NULL END) AS boldcnt, '.
+				'COUNT(CASE WHEN g.resourceurl LIKE "%ncbi%" THEN o.occid ELSE NULL END) AS gencnt, '.
+				'COUNT(CASE WHEN g.resourceurl NOT LIKE "%boldsystems%" AND g.resourceurl NOT LIKE "%ncbi%" THEN o.occid ELSE NULL END) AS geneticcnt '.
 				'FROM omoccurrences o INNER JOIN omoccurgenetic g ON o.occid = g.occid '.
 				'WHERE (o.collid IN('.$collid.')) ';
 			$rs = $this->conn->query($sql);
 			if($r = $rs->fetch_object()){
 				$statsArr['boldcnt'] = $r->boldcnt;
 				$statsArr['gencnt'] = $r->gencnt;
+				$statsArr['geneticcnt'] = $r->geneticcnt;
 			}
 			$rs->free();
 

collections/cleaning/taxonomycleaner.php

@@ -35,6 +35,7 @@
 	<head>
 		<title><?php echo $DEFAULT_TITLE; ?> Occurrence Taxon Cleaner</title>
 		<?php
+		$activateJQuery = true;
 		include_once($SERVER_ROOT.'/includes/head.php');
 		?>
 		<script src="../../js/jquery-3.2.1.min.js?ver=3" type="text/javascript"></script>