From 070436637b7e9bdbf6c8c7ca26065b317afee2f7 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Fri, 6 Sep 2019 13:29:31 -0700
Subject: [PATCH 01/23] Specimen Upload Adjustments

- Allow match-on-other-catalog-number variable to carried over from file upload to mapping forms (needed for NEON support)
- Misc spelling fixes
---
 collections/admin/specupload.php             | 15 ++++++++-------
 collections/specprocessor/imageprocessor.php | 15 ++++++---------
 2 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/collections/admin/specupload.php b/collections/admin/specupload.php
index 4084458150..22ba4a802a 100644
--- a/collections/admin/specupload.php
+++ b/collections/admin/specupload.php
@@ -18,7 +18,7 @@
 $importIdent = array_key_exists("importident",$_REQUEST)?true:false;
 $importImage = array_key_exists("importimage",$_REQUEST)?true:false;
 $matchCatNum = array_key_exists("matchcatnum",$_REQUEST)?true:false;
-$matchOtherCatNum = array_key_exists("matchothercatnum",$_REQUEST)?true:false;
+$matchOtherCatNum = array_key_exists('matchothercatnum',$_REQUEST)&&$_REQUEST['matchothercatnum']?true:false;
 $verifyImages = array_key_exists("verifyimages",$_REQUEST)&&$_REQUEST['verifyimages']?true:false;
 $processingStatus = array_key_exists("processingstatus",$_REQUEST)?$_REQUEST['processingstatus']:'';
 $finalTransfer = array_key_exists("finaltransfer",$_REQUEST)?$_REQUEST["finaltransfer"]:0;
@@ -539,7 +539,7 @@ function pkChanged(selObj){
 								Match on Catalog Number
 							</div>
 							<div style="margin:10px 0px;">
-								<input name="matchothercatnum" type="checkbox" value="1" />
+								<input name="matchothercatnum" type="checkbox" value="1" <?php echo ($matchOtherCatNum?'checked':''); ?> />
 								Match on Other Catalog Numbers
 							</div>
 							<ul style="margin:10px 0px;">
@@ -620,9 +620,10 @@ function pkChanged(selObj){
 									</div>
 									<div style="margin:10px;">
 										<input name="action" type="submit" value="Analyze File" />
-										<input name="uspid" type="hidden" value="<?php echo $uspid;?>" />
-										<input name="collid" type="hidden" value="<?php echo $collid;?>" />
-										<input name="uploadtype" type="hidden" value="<?php echo $uploadType;?>" />
+										<input name="uspid" type="hidden" value="<?php echo $uspid; ?>" />
+										<input name="collid" type="hidden" value="<?php echo $collid; ?>" />
+										<input name="uploadtype" type="hidden" value="<?php echo $uploadType; ?>" />
+										<input name="matchothercatnum" type="hidden" value="<?php echo $matchOtherCatNum; ?>" />
 										<input name="MAX_FILE_SIZE" type="hidden" value="100000000" />
 									</div>
 								</div>
@@ -786,7 +787,7 @@ function pkChanged(selObj){
 														Match on Catalog Number
 													</div>
 													<div>
-														<input name="matchothercatnum" type="checkbox" value="1" />
+														<input name="matchothercatnum" type="checkbox" value="1" <?php echo ($matchOtherCatNum?'checked':''); ?> />
 														Match on Other Catalog Numbers
 													</div>
 													<ul style="margin-top:2px">
@@ -942,7 +943,7 @@ function pkChanged(selObj){
 											Match on Catalog Number
 										</div>
 										<div>
-											<input name="matchothercatnum" type="checkbox" value="1" />
+											<input name="matchothercatnum" type="checkbox" value="1" <?php echo ($matchOtherCatNum?'checked':''); ?> />
 											Match on Other Catalog Numbers
 										</div>
 										<ul style="margin-top:2px">
diff --git a/collections/specprocessor/imageprocessor.php b/collections/specprocessor/imageprocessor.php
index 976febcf98..77058a9c8a 100644
--- a/collections/specprocessor/imageprocessor.php
+++ b/collections/specprocessor/imageprocessor.php
@@ -227,12 +227,9 @@ function validateFileUploadForm(f){
 		<!-- This is inner text! -->
 		<div id="innertext" style="background-color:white;">
 			<div style="padding:15px;">
-				These tools are designed to aid collection managers in batch processing specimen images.
-				Contact portal manager for helping in setting up a new workflow.
-				Once a profile is established, the collection manager can use this form to manually trigger image processing.
-				For more information, see the Symbiota documentation for
-				<b><a href="http://symbiota.org/docs/batch-loading-specimen-images-2/" target="_blank">recommended practices</a></b> for
-				integrating images.
+				These tools are designed to aid collection managers in batch processing specimen images. Contact portal manager for help in setting up a new workflow.
+				 Once a profile is established, the collection manager can use this form to manually trigger image processing. For more information, see the Symbiota documentation for
+				 <b><a href="http://symbiota.org/docs/batch-loading-specimen-images-2/" target="_blank">recommended practices</a></b> for integrating images.
 			</div>
 			<?php
 			if($SYMB_UID){
@@ -305,13 +302,13 @@ function validateFileUploadForm(f){
 										?>
 										<div>
 											<div style="width:180px;float:left;">
-												<b>Image Mapping Type:</b>
+												<b>Processing Type:</b>
 											</div>
 											<div style="float:left;">
 												<select name="projecttype" id="projecttype" onchange="uploadTypeChanged(this.form)" <?php echo ($spprid?'DISABLED':'');?>>
 													<option value="">----------------------</option>
 													<option value="local">Map Images from a Local or Remote Server</option>
-													<option value="file">Upload Image Map CSV File</option>
+													<option value="file">Image URL Mapping File</option>
 													<option value="idigbio">iDigBio Media Ingestion Report</option>
 													<option value="iplant">iPlant Image Harvest</option>
 												</select>
@@ -528,7 +525,7 @@ function validateFileUploadForm(f){
 									</div>
 									<div id="chooseFileDiv" class="profileDiv" style="clear:both;padding:15px 0px;display:none">
 										<div style="margin:5px 15px;">
-											<b>Select image mapping file:</b>
+											<b>Select URL mapping file:</b>
 											<input type='hidden' name='MAX_FILE_SIZE' value='20000000' />
 											<input name='uploadfile' type='file' size='70' value="Choose File" />
 										</div>

From bab2303863e8e3dcd2fed15ce82409e5e16bc2ac Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Sun, 8 Sep 2019 19:50:38 -0700
Subject: [PATCH 02/23] Paleo Module Development

- Make parent time fields auto-populate with appropriate terms
- Term adjustments: remove some terms and add others
- Misc bug fixes and layout adjustments
---
 classes/OccurrenceEditorManager.php           |  12 +-
 classes/OccurrenceEditorServices.php          |  21 ++
 classes/OccurrenceIndividualManager.php       |   2 +-
 collections/editor/includes/paleoinclude.php  | 191 +++++++++++-------
 collections/editor/rpc/getPaleoGtsParents.php |  12 ++
 collections/individual/index.php              |   2 +-
 .../dev/db_schema_patch_pending.sql           |   4 +-
 css/occureditor.css                           |   2 +-
 8 files changed, 165 insertions(+), 81 deletions(-)
 create mode 100644 collections/editor/rpc/getPaleoGtsParents.php

diff --git a/classes/OccurrenceEditorManager.php b/classes/OccurrenceEditorManager.php
index 27629cbe3d..9093c3dc0b 100644
--- a/classes/OccurrenceEditorManager.php
+++ b/classes/OccurrenceEditorManager.php
@@ -99,7 +99,6 @@ public function getDynamicPropertiesArr(){
 
 	//Query functions
 	public function setQueryVariables($overrideQry = false){
-		global $CLIENT_ROOT;
 		if($overrideQry){
 			$this->qryArr = $overrideQry;
 			unset($_SESSION['editorquery']);
@@ -558,7 +557,6 @@ private function setSqlOrderBy(&$sql){
 	}
 
 	public function getQueryRecordCount($reset = 0){
-		global $CLIENT_ROOT;
 		if(!$reset && array_key_exists('rc',$this->qryArr)) return $this->qryArr['rc'];
 		$recCnt = false;
 		if($this->sqlWhere){
@@ -771,7 +769,7 @@ public function editOccurrence($occArr, $editorStatus){
 			if($editArr || $quickHostEntered){
 				if($editArr){
 					//Deal with scientific name changes if the AJAX code fails
-					$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biozone',
+					$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
 						'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
 					if(in_array('sciname',$editArr) && $occArr['sciname'] && !$occArr['tidinterpreted']){
 						$sql2 = 'SELECT t.tid, t.author, ts.family '.
@@ -921,7 +919,7 @@ public function editOccurrence($occArr, $editorStatus){
 								if($paleoRS->num_rows) $paleoRecordExist = true;
 								$paleoRS->free();
 							}
-							$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biozone',
+							$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
 								'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
 							if($paleoRecordExist){
 								//Edit existing record
@@ -1077,7 +1075,7 @@ public function addOccurrence($occArr){
 				}
 				//Deal with paleo
 				if(in_array('eon',$occArr)){
-					$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biozone',
+					$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
 						'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
 					//Add new record
 					$paleoFrag1 = '';
@@ -1550,7 +1548,7 @@ public function batchUpdateField($fieldName,$oldValue,$newValue,$buMatch){
 					$statusStr = 'ERROR adding update to omoccuredits: '.$this->conn->error;
 				}
 				//Apply edits to core tables
-				$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biozone',
+				$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
 					'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
 				if(array_key_exists($fn, $paleoFieldArr)){
 					$sql = 'UPDATE omoccurpaleo SET '.$fn.' = '.$nvSqlFrag.' '.$sqlWhere;
@@ -1607,7 +1605,7 @@ public function carryOverValues($fArr){
 			'georeferencesources','georeferenceverificationstatus','georeferenceremarks',
 			'minimumelevationinmeters','maximumelevationinmeters','verbatimelevation','minimumdepthinmeters','maximumdepthinmeters','verbatimdepth',
 			'habitat','substrate','lifestage', 'sex', 'individualcount', 'samplingprotocol', 'preparations',
-			'associatedtaxa','basisofrecord','language','labelproject','eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biozone',
+			'associatedtaxa','basisofrecord','language','labelproject','eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
 			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element');
 		$retArr = $this->cleanOutArr(array_intersect_key($fArr,array_flip($locArr)));
 		return $retArr;
diff --git a/classes/OccurrenceEditorServices.php b/classes/OccurrenceEditorServices.php
index a94aef00e0..8813387fce 100644
--- a/classes/OccurrenceEditorServices.php
+++ b/classes/OccurrenceEditorServices.php
@@ -28,6 +28,27 @@ public function getSpeciesSuggest($term){
 		return $retArr;
 	}
 
+	public function getPaleoGtsParents($term){
+		$retArr = Array();
+		$sql = 'SELECT gtsid, gtsterm, rankid, rankname, parentgtsid FROM omoccurpaleogts WHERE gtsterm = "'.$this->cleanInStr($term).'"';
+		$parentId = '';
+		do{
+			$rs = $this->conn->query($sql);
+			if ($r = $rs->fetch_object()){
+				if($parentId == $r->parentgtsid){
+					$parentId = 0;
+				}
+				else{
+					$retArr[] = array("rankid" => [$r->rankid], "value" => $r->gtsterm);
+					$parentId = $r->parentgtsid;
+				}
+			}
+			$rs->free();
+			$sql = 'SELECT gtsid, gtsterm, rankid, rankname, parentgtsid FROM omoccurpaleogts WHERE gtsid = '.$parentId;
+		}while($parentId);
+		return $retArr;
+	}
+
 	//Misc functions
 	protected function cleanInStr($str){
 		$newStr = trim($str);
diff --git a/classes/OccurrenceIndividualManager.php b/classes/OccurrenceIndividualManager.php
index 0702c4c249..b865b2a254 100644
--- a/classes/OccurrenceIndividualManager.php
+++ b/classes/OccurrenceIndividualManager.php
@@ -219,7 +219,7 @@ private function loadImages(){
 	}
 
 	private function loadPaleo(){
-		$sql = 'SELECT paleoid, eon, era, period, epoch, earlyinterval, lateinterval, absoluteage, storageage, stage, localstage, biozone, '.
+		$sql = 'SELECT paleoid, eon, era, period, epoch, earlyinterval, lateinterval, absoluteage, storageage, stage, localstage, biota, '.
 			'biostratigraphy, lithogroup, formation, taxonenvironment, member, lithology, stratremarks, lithdescription, element, slideproperties '.
 			'FROM omoccurpaleo WHERE occid = '.$this->occid;
 		$rs = $this->conn->query($sql);
diff --git a/collections/editor/includes/paleoinclude.php b/collections/editor/includes/paleoinclude.php
index a7e701581e..989fad1fbc 100644
--- a/collections/editor/includes/paleoinclude.php
+++ b/collections/editor/includes/paleoinclude.php
@@ -4,16 +4,16 @@
 <script>
 	var gtsArr = { <?php $d=''; foreach($gtsTermArr as $term => $rankid){ echo $d.'"'.$term.'":'.$rankid; $d=','; } ?> };
 	function earlyIntervalChanged(elemObj){
-		intervalChanged(elemObj);
+		paloIntervalChanged(elemObj);
 		fieldChanged('earlyInterval');
 	}
 
 	function lateIntervalChanged(elemObj){
-		intervalChanged(elemObj);
+		paloIntervalChanged(elemObj);
 		fieldChanged('lateInterval');
 	}
 
-	function intervalChanged(elemObj){
+	function paloIntervalChanged(elemObj){
 		var term = elemObj.value;
 		var rankid = gtsArr[term];
 		if(rankid==10 || rankid==20){
@@ -21,53 +21,74 @@ function intervalChanged(elemObj){
 		}
 		else if(rankid==30){
 			if($("select[name=era]").val() == '') $("select[name=era]").val(term);
+			setPaloParents("era");
 		}
 		else if(rankid==40){
 			if($("select[name=period]").val() == '') $("select[name=period]").val(term);
+			setPaloParents("period");
 		}
 		else if(rankid==50){
 			if($("select[name=epoch]").val() == '') $("select[name=epoch]").val(term);
+			setPaloParents("epoch");
 		}
 		else if(rankid==60){
 			if($("select[name=stage]").val() == '') $("select[name=stage]").val(term);
+			setPaloParents("stage");
+		}
+	}
+
+	function setPaloParents(timePeriod){
+		if(timePeriod){
+			fieldChanged(timePeriod);
+			switch(timePeriod) {
+				case "eon":
+					$("select[name=era]").val("");
+				case "era":
+					$("select[name=period]").val("");
+				case "period":
+					$("select[name=epoch]").val("");
+				case "epoch":
+					$("select[name=stage]").val("");
+			}
+			var childValue = $("select[name="+timePeriod+"]").val();
+			if(childValue){
+				if($("select[name=earlyInterval]").val() == "") $("select[name=earlyInterval]").val(childValue);
+				if($("select[name=lateInterval]").val() == "") $("select[name=lateInterval]").val(childValue);
+				if(timePeriod != "eon"){
+					$.ajax({
+						type: "POST",
+						url: "rpc/getPaleoGtsParents.php",
+						dataType: "json",
+						data: { term: childValue }
+					}).done(function( gtsObj ) {
+					  	for (i = 0; i < gtsObj.length; i++) {
+					  		var rankid = gtsObj[i].rankid;
+							if(rankid == 10 || rankid == 20){
+								$("select[name=eon]").val(gtsObj[i].value);
+							}
+							else if(rankid == 30){
+								$("select[name=era]").val(gtsObj[i].value);
+							}
+							else if(rankid == 40){
+								$("select[name=period]").val(gtsObj[i].value);
+							}
+							else if(rankid == 50){
+								$("select[name=epoch]").val(gtsObj[i].value);
+							}
+					  	}
+					});
+				}
+			}
 		}
 	}
 </script>
 <fieldset>
 	<legend><b>Paleontology</b></legend>
-	<div>
-		<div id="earlyIntervalDiv">
-			<?php echo (defined('EARLYINTERVALLABEL')?EARLYINTERVALLABEL:'Early Interval'); ?>
-			<a href="#" onclick="return dwcDoc('earlyInterval')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="earlyInterval" onchange="earlyIntervalChanged(this)">
-				<option value=""></option>
-				<?php
-				foreach($gtsTermArr as $term => $rankid){
-					echo '<option value="'.$term.'" '.(isset($occArr['earlyInterval']) && $occArr['earlyInterval']==$term?'SELECTED':'').'>'.$term.'</option>';
-				}
-				?>
-			</select>
-			<!-- <input type="text" name="earlyInterval" value="<?php echo isset($occArr['earlyInterval'])?$occArr['earlyInterval']:''; ?>" onchange="fieldChanged('earlyInterval');" /> -->
-		</div>
-		<div id="lateIntervalDiv">
-			<?php echo (defined('LATEINTERVALLABEL')?LATEINTERVALLABEL:'Late Interval'); ?>
-			<a href="#" onclick="return dwcDoc('lateInterval')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="lateInterval" onchange="lateIntervalChanged(this)">
-				<option value=""></option>
-				<?php
-				foreach($gtsTermArr as $term => $rankid){
-					echo '<option value="'.$term.'" '.(isset($occArr['lateInterval']) && $occArr['lateInterval']==$term?'SELECTED':'').'>'.$term.'</option>';
-				}
-				?>
-			</select>
-			<!-- <input type="text" name="lateInterval" value="<?php echo isset($occArr['lateInterval'])?$occArr['lateInterval']:''; ?>" onchange="fieldChanged('lateInterval');" /> -->
-		</div>
-	</div>
 	<div style="clear:both">
 		<div id="eonDiv">
 			<?php echo (defined('EONLABEL')?EONLABEL:'Eon'); ?>
-			<a href="#" onclick="return dwcDoc('eon')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="eon" onchange="fieldChanged('eon');">
+			<a href="#" onclick="return dwcDoc('eon')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<select name="eon" onchange="setPaloParents('eon');">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid ){
@@ -79,8 +100,8 @@ function intervalChanged(elemObj){
 		</div>
 		<div id="eraDiv">
 			<?php echo (defined('ERALABEL')?ERALABEL:'Era'); ?>
-			<a href="#" onclick="return dwcDoc('era')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="era" onchange="fieldChanged('era');">
+			<a href="#" onclick="return dwcDoc('era')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<select name="era" onchange="setPaloParents('era');">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid ){
@@ -92,8 +113,8 @@ function intervalChanged(elemObj){
 		</div>
 		<div id="periodDiv">
 			<?php echo (defined('PERIODLABEL')?PERIODLABEL:'Period'); ?>
-			<a href="#" onclick="return dwcDoc('period')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="period" onchange="fieldChanged('period');">
+			<a href="#" onclick="return dwcDoc('period')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<select name="period" onchange="setPaloParents('period');">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid){
@@ -105,8 +126,8 @@ function intervalChanged(elemObj){
 		</div>
 		<div id="epochDiv">
 			<?php echo (defined('EPOCHLABEL')?EPOCHLABEL:'Epoch'); ?>
-			<a href="#" onclick="return dwcDoc('epoch')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="epoch" onchange="fieldChanged('epoch');">
+			<a href="#" onclick="return dwcDoc('epoch')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<select name="epoch" onchange="setPaloParents('epoch');">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid){
@@ -118,8 +139,8 @@ function intervalChanged(elemObj){
 		</div>
 		<div id="stageDiv">
 			<?php echo (defined('STAGELABEL')?STAGELABEL:'Stage'); ?>
-			<a href="#" onclick="return dwcDoc('stage')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="stage" onchange="fieldChanged('stage');">
+			<a href="#" onclick="return dwcDoc('stage')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<select name="stage" onchange="setPaloParents('stage');">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid){
@@ -130,10 +151,38 @@ function intervalChanged(elemObj){
 			<!-- <input type="text" name="stage" value="<?php echo isset($occArr['stage'])?$occArr['stage']:''; ?>" onchange="fieldChanged('stage');" />  -->
 		</div>
 	</div>
+	<div>
+		<div id="earlyIntervalDiv">
+			<?php echo (defined('EARLYINTERVALLABEL')?EARLYINTERVALLABEL:'Early Interval'); ?>
+			<a href="#" onclick="return dwcDoc('earlyInterval')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<select name="earlyInterval" onchange="earlyIntervalChanged(this)">
+				<option value=""></option>
+				<?php
+				foreach($gtsTermArr as $term => $rankid){
+					echo '<option value="'.$term.'" '.(isset($occArr['earlyInterval']) && $occArr['earlyInterval']==$term?'SELECTED':'').'>'.$term.'</option>';
+				}
+				?>
+			</select>
+			<!-- <input type="text" name="earlyInterval" value="<?php echo isset($occArr['earlyInterval'])?$occArr['earlyInterval']:''; ?>" onchange="fieldChanged('earlyInterval');" /> -->
+		</div>
+		<div id="lateIntervalDiv">
+			<?php echo (defined('LATEINTERVALLABEL')?LATEINTERVALLABEL:'Late Interval'); ?>
+			<a href="#" onclick="return dwcDoc('lateInterval')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<select name="lateInterval" onchange="lateIntervalChanged(this)">
+				<option value=""></option>
+				<?php
+				foreach($gtsTermArr as $term => $rankid){
+					echo '<option value="'.$term.'" '.(isset($occArr['lateInterval']) && $occArr['lateInterval']==$term?'SELECTED':'').'>'.$term.'</option>';
+				}
+				?>
+			</select>
+			<!-- <input type="text" name="lateInterval" value="<?php echo isset($occArr['lateInterval'])?$occArr['lateInterval']:''; ?>" onchange="fieldChanged('lateInterval');" /> -->
+		</div>
+	</div>
 	<div style="clear:both">
 		<div id="absoluteAgeDiv">
 			<?php echo (defined('ABSOLUTEAGELABEL')?ABSOLUTEAGELABEL:'Absolute Age'); ?>
-			<a href="#" onclick="return dwcDoc('absoluteAge')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('absoluteAge')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<select name="absoluteAge" onchange="fieldChanged('absoluteAge');">
 				<option value=""></option>
 				<?php
@@ -146,7 +195,7 @@ function intervalChanged(elemObj){
 		</div>
 		<div id="storageAgeDiv">
 			<?php echo (defined('STORAGEAGELABEL')?STORAGEAGELABEL:'Storage Age'); ?>
-			<a href="#" onclick="return dwcDoc('storageAge')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('storageAge')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<select name="storageAge" onchange="fieldChanged('storageAge');">
 				<option value=""></option>
 				<?php
@@ -159,36 +208,47 @@ function intervalChanged(elemObj){
 		</div>
 		<div id="localStageDiv">
 			<?php echo (defined('LOCALSTAGELABEL')?LOCALSTAGELABEL:'Local Stage'); ?>
-			<a href="#" onclick="return dwcDoc('localStage')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('localStage')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="localStage" value="<?php echo isset($occArr['localStage'])?$occArr['localStage']:''; ?>" onchange="fieldChanged('localStage');" />
 		</div>
 	</div>
 	<div style="clear:both">
-		<div id="biozoneDiv">
-			<?php echo (defined('BIOZONELABEL')?BIOZONELABEL:'Biozone'); ?>
-			<a href="#" onclick="return dwcDoc('biozone')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<input type="text" name="biozone" value="<?php echo isset($occArr['biozone'])?$occArr['biozone']:''; ?>" onchange="fieldChanged('biozone');" />
+		<div id="biotaDiv">
+			<?php echo (defined('BIOTALABEL')?BIOTALABEL:'Biota (Flora/Fauna)'); ?>
+			<a href="#" onclick="return dwcDoc('biota')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<input type="text" name="biota" value="<?php echo isset($occArr['biota'])?$occArr['biota']:''; ?>" onchange="fieldChanged('biota');" />
 		</div>
 		<div id="biostratigraphyDiv">
-			<?php echo (defined('BIOSTRATIGRAPHYLABEL')?BIOSTRATIGRAPHYLABEL:'Biostratigraphy (Flora/Fauna)'); ?>
-			<a href="#" onclick="return dwcDoc('biostratigraphy')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<?php echo (defined('BIOSTRATIGRAPHYLABEL')?BIOSTRATIGRAPHYLABEL:'Biostratigraphy (Biozone)'); ?>
+			<a href="#" onclick="return dwcDoc('biostratigraphy')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="biostratigraphy" value="<?php echo isset($occArr['biostratigraphy'])?$occArr['biostratigraphy']:''; ?>" onchange="fieldChanged('biostratigraphy');" />
 		</div>
+		<div id="taxonEnvironmentDiv">
+			<?php echo (defined('TAXONENVIRONMENTLABEL')?TAXONENVIRONMENTLABEL:'Taxon Environment (Formation Marine)'); ?>
+			<a href="#" onclick="return dwcDoc('taxonEnvironment')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<?php
+			$taxonEnvir = '';
+			if(isset($occArr['taxonEnvironment'])) $taxonEnvir = $occArr['taxonEnvironment'];
+			?>
+			<select name="taxonEnvironment" onchange="fieldChanged('taxonEnvironment');">
+				<option value="">----------------</option>
+				<option <?php if($taxonEnvir=='marine') echo 'SELECTED'; ?>>marine</option>
+				<option<?php if($taxonEnvir=='non-marine') echo 'SELECTED'; ?>>non-marine</option>
+				<option<?php if($taxonEnvir=='marine and non-marine') echo 'SELECTED'; ?>>marine and non-marine</option>
+			</select>
+		</div>
+	</div>
+	<div style="clear:both">
 		<div id="lithoGroupDiv">
 			<?php echo (defined('LITHOGROUPLABEL')?LITHOGROUPLABEL:'Group'); ?>
-			<a href="#" onclick="return dwcDoc('group')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('group')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="lithogroup" value="<?php echo isset($occArr['lithogroup'])?$occArr['lithogroup']:''; ?>" onchange="fieldChanged('lithogroup');" />
 		</div>
 		<div id="formationDiv">
 			<?php echo (defined('FORMATIONLABEL')?FORMATIONLABEL:'Formation'); ?>
-			<a href="#" onclick="return dwcDoc('formation')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('formation')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="formation" value="<?php echo isset($occArr['formation'])?$occArr['formation']:''; ?>" onchange="fieldChanged('formation');" />
 		</div>
-		<div id="taxonEnvironmentDiv">
-			<?php echo (defined('TAXONENVIRONMENTLABEL')?TAXONENVIRONMENTLABEL:'Taxon Environment (Formation Marine)'); ?>
-			<a href="#" onclick="return dwcDoc('taxonEnvironment')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<input type="text" name="taxonEnvironment" value="<?php echo isset($occArr['taxonEnvironment'])?$occArr['taxonEnvironment']:''; ?>" onchange="fieldChanged('taxonEnvironment');" />
-		</div>
 		<div id="memberDiv">
 			<?php echo (defined('MEMBERLABEL')?MEMBERLABEL:'Member'); ?>
 			<a href="#" onclick="return dwcDoc('member')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
@@ -196,33 +256,26 @@ function intervalChanged(elemObj){
 		</div>
 		<div id="lithologyDiv">
 			<?php echo (defined('LITHOLOGYLABEL')?LITHOLOGYLABEL:'Lithology'); ?>
-			<a href="#" onclick="return dwcDoc('lithology')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('lithology')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="lithology" value="<?php echo isset($occArr['lithology'])?$occArr['lithology']:''; ?>" onchange="fieldChanged('lithology');" />
 		</div>
 	</div>
 	<div style="clear:both">
 		<div id="stratRemarksDiv">
-			<?php echo (defined('TAXONENVIRONMENTLABEL')?TAXONENVIRONMENTLABEL:'Stratigraphy Remarks'); ?>
-			<a href="#" onclick="return dwcDoc('stratRemarks')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<?php echo (defined('TAXONENVIRONMENTLABEL')?TAXONENVIRONMENTLABEL:'Remarks'); ?>
+			<a href="#" onclick="return dwcDoc('stratRemarks')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="stratRemarks" value="<?php echo isset($occArr['stratRemarks'])?$occArr['stratRemarks']:''; ?>" onchange="fieldChanged('stratRemarks');" />
 		</div>
 	</div>
-	<div style="clear:both">
-		<div id="lithDescriptionDiv">
-			<?php echo (defined('LITHDESCRIPTIONLABEL')?TAXONENVIRONMENTLABEL:'Lithology Description'); ?>
-			<a href="#" onclick="return dwcDoc('lithDescription')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<input type="text" name="lithDescription" value="<?php echo isset($occArr['lithDescription'])?$occArr['lithDescription']:''; ?>" onchange="fieldChanged('lithDescription');" />
-		</div>
-	</div>
 	<div style="clear:both">
 		<div id="elementDiv">
 			<?php echo (defined('ELEMENTLABEL')?ELEMENTLABEL:'Element'); ?>
-			<a href="#" onclick="return dwcDoc('element')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('element')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="element" value="<?php echo isset($occArr['element'])?$occArr['element']:''; ?>" onchange="fieldChanged('element');" />
 		</div>
 		<div id="slidePropertiesDiv">
 			<?php echo (defined('SLIDEPROPERTIESLABEL')?SLIDEPROPERTIESLABEL:'Slide Properties'); ?>
-			<a href="#" onclick="return dwcDoc('slideProperties')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('slideProperties')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="slideProperties" value="<?php echo isset($occArr['slideProperties'])?$occArr['slideProperties']:''; ?>" onchange="fieldChanged('slideProperties');" />
 		</div>
 	</div>
diff --git a/collections/editor/rpc/getPaleoGtsParents.php b/collections/editor/rpc/getPaleoGtsParents.php
new file mode 100644
index 0000000000..821380aa36
--- /dev/null
+++ b/collections/editor/rpc/getPaleoGtsParents.php
@@ -0,0 +1,12 @@
+<?php
+include_once('../../../config/symbini.php');
+include_once($SERVER_ROOT.'/classes/OccurrenceEditorServices.php');
+header("Content-Type: application/json; charset=".$CHARSET);
+
+$term = $_REQUEST['term'];
+
+$searchManager = new OccurrenceEditorServices();
+$retArr = $searchManager->getPaleoGtsParents($term);
+
+echo json_encode($retArr);
+?>
\ No newline at end of file
diff --git a/collections/individual/index.php b/collections/individual/index.php
index 010b5e7c13..45983a510e 100644
--- a/collections/individual/index.php
+++ b/collections/individual/index.php
@@ -776,7 +776,7 @@ function initializeMap(){
 								if($occArr['storageage']) $paleoStr .= '; <b>storage age:</b> '.$occArr['storageage'];
 								if($occArr['stage']) $paleoStr .= '; <b>stage:</b> '.$occArr['stage'];
 								if($occArr['localstage']) $paleoStr .= '; <b>local stage:</b> '.$occArr['localstage'];
-								if($occArr['biozone']) $paleoStr .= '; <b>biozone:</b> '.$occArr['biozone'];
+								if($occArr['biota']) $paleoStr .= '; <b>biota:</b> '.$occArr['biota'];
 								if($occArr['biostratigraphy']) $paleoStr .= '; <b>biostratigraphy:</b> '.$occArr['biostratigraphy'];
 								if($occArr['lithogroup']) $paleoStr .= '; <b>group:</b> '.$occArr['lithogroup'];
 								if($occArr['formation']) $paleoStr .= '; <b>formation:</b> '.$occArr['formation'];
diff --git a/config/schema-1.0/dev/db_schema_patch_pending.sql b/config/schema-1.0/dev/db_schema_patch_pending.sql
index 743cd9a064..acdfeac583 100644
--- a/config/schema-1.0/dev/db_schema_patch_pending.sql
+++ b/config/schema-1.0/dev/db_schema_patch_pending.sql
@@ -74,8 +74,8 @@ CREATE TABLE `omoccurpaleo` (
   `storageAge` VARCHAR(65) NULL,
   `stage` VARCHAR(65) NULL,
   `localStage` VARCHAR(65) NULL,
-  `biozone` VARCHAR(130) NULL,
-  `biostratigraphy` VARCHAR(65) NULL COMMENT 'Flora or Fanua',
+  `biota` VARCHAR(65) NULL COMMENT 'Flora or Fanua',
+  `biostratigraphy` VARCHAR(65) NULL COMMENT 'Biozone',
   `lithogroup` VARCHAR(65) NULL,
   `formation` VARCHAR(65) NULL,
   `taxonEnvironment` VARCHAR(65) NULL COMMENT 'Marine or not',
diff --git a/css/occureditor.css b/css/occureditor.css
index 29af2735c2..709779275b 100644
--- a/css/occureditor.css
+++ b/css/occureditor.css
@@ -811,7 +811,7 @@ body{
 #storageAgeDiv{ float:left; margin:3px; }
 #stageDiv{ float:left; margin:3px; }
 #localStageDiv{ float:left; margin:3px; }
-#biozoneDiv{ float:left; margin:3px; }
+#biotaDiv{ float:left; margin:3px; }
 #biostratigraphyDiv{ float:left; margin:3px; }
 #lithoGroupDiv{ float:left; margin:3px; }
 #formationDiv{ float:left; margin:3px; }

From a7f56b771c0295df2e37c9fd43d32355d46b198c Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Mon, 9 Sep 2019 16:07:06 -0700
Subject: [PATCH 03/23] Paleo Module Developments

- Debug adding new paleo records
- Debug updating an existing paleo record
---
 classes/ImageLibraryManager.php              | 18 ++++--
 classes/OccurrenceEditorManager.php          | 66 +++++++++++++-------
 collections/editor/includes/paleoinclude.php | 34 +++++-----
 3 files changed, 70 insertions(+), 48 deletions(-)

diff --git a/classes/ImageLibraryManager.php b/classes/ImageLibraryManager.php
index 0a071f8c7b..77f51ebf1f 100644
--- a/classes/ImageLibraryManager.php
+++ b/classes/ImageLibraryManager.php
@@ -498,12 +498,20 @@ public function getTaxaSuggest($queryString, $type = 'sciname'){
 
 	public function getPhotographerUidArr(){
 		$retArr = array();
-		$sql = 'SELECT DISTINCT u.uid, CONCAT_WS(", ",u.lastname, u.firstname) AS fullname FROM images i INNER JOIN users u ON i.photographeruid = u.uid ';
-		$rs = $this->conn->query($sql);
-		while ($r = $rs->fetch_object()) {
-			$retArr[$r->uid] = $r->fullname;
+		$sql1 = 'SELECT DISTINCT photographeruid FROM images WHERE photographeruid IS NOT NULL';
+		$rs1 = $this->conn->query($sql1);
+		while ($r1 = $rs1->fetch_object()) {
+			$retArr[$r1->photographeruid] = '';
+		}
+		$rs1->free();
+		if($retArr){
+			$sql2 = 'SELECT uid, CONCAT_WS(", ", lastname, firstname) AS fullname FROM users WHERE uid IN('.implode(',',array_keys($retArr)).')';
+			$rs2 = $this->conn->query($sql2);
+			while ($r2 = $rs2->fetch_object()) {
+				$retArr[$r2->uid] = $r2->fullname;
+			}
+			$rs2->free();
 		}
-		$rs->free();
 		asort($retArr,SORT_NATURAL | SORT_FLAG_CASE);
 		return $retArr;
 	}
diff --git a/classes/OccurrenceEditorManager.php b/classes/OccurrenceEditorManager.php
index 9093c3dc0b..ecb9528aed 100644
--- a/classes/OccurrenceEditorManager.php
+++ b/classes/OccurrenceEditorManager.php
@@ -17,6 +17,7 @@ class OccurrenceEditorManager {
 
 	protected $occurrenceMap = array();
 	private $occFieldArr = array();
+	private $paleoFieldArr = array();
 	private $sqlWhere;
 	private $otherCatNumIsNum = false;
 	private $qryArr = array();
@@ -47,6 +48,8 @@ public function __construct($conn = null){
 			'minimumdepthinmeters', 'maximumdepthinmeters', 'verbatimdepth', 'disposition', 'language', 'duplicatequantity', 'genericcolumn1', 'genericcolumn2',
 			'labelproject','observeruid','basisofrecord','institutioncode','collectioncode','ownerinstitutioncode','datelastmodified', 'processingstatus',
 			'recordenteredby', 'dateentered');
+		$this->paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
+			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
 	}
 
 	public function __destruct(){
@@ -92,7 +95,7 @@ public function getDynamicPropertiesArr(){
 			$dynPropArr = json_decode($this->collMap['dynamicproperties'],true);
 			if(isset($dynPropArr['editorProp'])) $propArr = $dynPropArr['editorProp'];
 		}
-		//$dynPropArr = array("editorProp"=>array("paleoMod"=>1,"catalogDupeCheck"=>1));
+		$dynPropArr = array("editorProp"=>array("paleoMod"=>1,"catalogDupeCheck"=>1));
 		if(isset($dynPropArr['editorProp'])) $propArr = $dynPropArr['editorProp'];
 		return $propArr;
 	}
@@ -687,6 +690,7 @@ protected function setOccurArr($start = 0, $limit = 0){
 			$this->occurrenceMap = $this->cleanOutArr($retArr);
 			if($this->occid){
 				$this->setLoanData();
+				$this->setPaleoData();
 				if(isset($GLOBALS['ACTIVATE_EXSICCATI']) && $GLOBALS['ACTIVATE_EXSICCATI']) $this->setExsiccati();
 			}
 		}
@@ -769,8 +773,6 @@ public function editOccurrence($occArr, $editorStatus){
 			if($editArr || $quickHostEntered){
 				if($editArr){
 					//Deal with scientific name changes if the AJAX code fails
-					$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-						'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
 					if(in_array('sciname',$editArr) && $occArr['sciname'] && !$occArr['tidinterpreted']){
 						$sql2 = 'SELECT t.tid, t.author, ts.family '.
 							'FROM taxa t INNER JOIN taxstatus ts ON t.tid = ts.tid '.
@@ -799,7 +801,7 @@ public function editOccurrence($occArr, $editorStatus){
 						(in_array('recordenteredby',$editArr)?'':',recordenteredby').
 						' FROM omoccurrences o ';
 					}
-					if(array_intersect($editArr, $paleoFieldArr)){
+					if(array_intersect($editArr, $this->paleoFieldArr)){
 						$sql .= 'LEFT JOIN omoccurpaleo p ON o.occid = p.occid ';
 					}
 					$sql .= 'WHERE o.occid = '.$occArr['occid'];
@@ -919,40 +921,49 @@ public function editOccurrence($occArr, $editorStatus){
 								if($paleoRS->num_rows) $paleoRecordExist = true;
 								$paleoRS->free();
 							}
-							$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-								'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
 							if($paleoRecordExist){
 								//Edit existing record
 								$paleoHasValue = false;
 								$paleoFrag = '';
-								foreach($paleoFieldArr as $paleoField){
+								foreach($this->paleoFieldArr as $paleoField){
 									if(array_key_exists($paleoField,$occArr)){
 										$paleoFrag .= ','.$paleoField.' = '.($occArr[$paleoField]?'"'.$this->cleanInStr($occArr[$paleoField]).'"':'NULL');
 										if($occArr[$paleoField]) $paleoHasValue = true;
 									}
 								}
+								$paleoSql = '';
 								if($paleoHasValue){
-									if($paleoFrag) $this->conn->query('UPDATE omoccurpaleo SET '.substr($paleoFrag, 1).' WHERE occid = '.$occArr['occid']);
+									if($paleoFrag) $paleoSql = 'UPDATE omoccurpaleo SET '.substr($paleoFrag, 1).' WHERE occid = '.$occArr['occid'];
+									$this->conn->query('UPDATE omoccurpaleo SET '.substr($paleoFrag, 1).' WHERE occid = '.$occArr['occid']);
 								}
 								else{
-									$this->conn->query('DELETE FROM omoccurpaleo WHERE occid = '.$occArr['occid']);
+									$paleoSql = 'DELETE FROM omoccurpaleo WHERE occid = '.$occArr['occid'];
+								}
+								if($paleoSql){
+									if(!$this->conn->query($paleoSql)){
+										$status = 'ERROR editing paleo data: '.$this->conn->error;
+									}
 								}
 							}
 							else{
 								//Add new record
 								$paleoFrag1 = '';
 								$paleoFrag2 = '';
-								foreach($paleoFieldArr as $paleoField){
+								foreach($this->paleoFieldArr as $paleoField){
 									if(array_key_exists($paleoField,$occArr) && $occArr[$paleoField]){
 										$paleoFrag1 .= ','.$paleoField;
 										$paleoFrag2 .= ',"'.$this->cleanInStr($occArr[$paleoField]).'" ';
 									}
 								}
 								if($paleoFrag1){
-									$this->conn->query('INSERT INTO omoccurpaleo(occid'.$paleoFrag1.') VALUES('.$occArr['occid'].$paleoFrag2.')');
+									$paleoSql = 'INSERT INTO omoccurpaleo(occid'.$paleoFrag1.') VALUES('.$occArr['occid'].$paleoFrag2.')';
+									if(!$this->conn->query($paleoSql)){
+										$status = 'ERROR adding new record for paleo data edit: '.$this->conn->error;
+									}
 								}
 							}
 						}
+
 						//Deal with exsiccati
 						if(in_array('ometid',$editArr) || in_array('exsnumber',$editArr)){
 							$ometid = $this->cleanInStr($occArr['ometid']);
@@ -1062,7 +1073,6 @@ public function addOccurrence($occArr){
 				}
 			}
 			$sql .= ')';
-			//echo "<div>".$sql."</div>";
 			if($this->conn->query($sql)){
 				$this->occid = $this->conn->insert_id;
 				//Update collection stats
@@ -1074,20 +1084,19 @@ public function addOccurrence($occArr){
 					$status .= '(WARNING: Symbiota GUID mapping failed) ';
 				}
 				//Deal with paleo
-				if(in_array('eon',$occArr)){
-					$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-						'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
+				if(array_key_exists('eon',$occArr)){
 					//Add new record
 					$paleoFrag1 = '';
 					$paleoFrag2 = '';
-					foreach($paleoFieldArr as $paleoField){
+					foreach($this->paleoFieldArr as $paleoField){
 						if(array_key_exists($paleoField,$occArr)){
-							$paleoFrag1 = ','.$paleoField;
+							$paleoFrag1 .= ','.$paleoField;
 							$paleoFrag2 .= ','.($occArr[$paleoField]?'"'.$this->cleanInStr($occArr[$paleoField]).'"':'NULL');
 						}
 					}
 					if($paleoFrag1){
-						$this->conn->query('INSERT INTO omoccurpaleo(occid'.$paleoFrag1.') VALUES('.$this->occid.$paleoFrag2.')');
+						$paleoSql = 'INSERT INTO omoccurpaleo(occid'.$paleoFrag1.') VALUES('.$this->occid.$paleoFrag2.')';
+						$this->conn->query($paleoSql);
 					}
 				}
 				//Deal with Exsiccati
@@ -1461,6 +1470,18 @@ private function setLoanData(){
 		$rs->free();
 	}
 
+	private function setPaleoData(){
+		$sql = 'SELECT '.implode(',',$this->paleoFieldArr).' FROM omoccurpaleo WHERE occid = '.$this->occid;
+		//echo $sql;
+		$rs = $this->conn->query($sql);
+		if($r = $rs->fetch_assoc()){
+			foreach($this->paleoFieldArr as $term){
+				$this->occurrenceMap[$this->occid][$term] = $r[$term];
+			}
+		}
+		$rs->free();
+	}
+
 	private function setExsiccati(){
 		$sql = 'SELECT l.notes, l.ranking, l.omenid, n.exsnumber, t.ometid, t.title, t.abbreviation, t.editor '.
 			'FROM omexsiccatiocclink l INNER JOIN omexsiccatinumbers n ON l.omenid = n.omenid '.
@@ -1548,9 +1569,7 @@ public function batchUpdateField($fieldName,$oldValue,$newValue,$buMatch){
 					$statusStr = 'ERROR adding update to omoccuredits: '.$this->conn->error;
 				}
 				//Apply edits to core tables
-				$paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-					'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
-				if(array_key_exists($fn, $paleoFieldArr)){
+				if(array_key_exists($fn, $this->paleoFieldArr)){
 					$sql = 'UPDATE omoccurpaleo SET '.$fn.' = '.$nvSqlFrag.' '.$sqlWhere;
 				}
 				else{
@@ -2084,9 +2103,8 @@ public function getCollectionList(){
 		$collArr = array('0');
 		if(isset($GLOBALS['USER_RIGHTS']['CollAdmin'])) $collArr = $GLOBALS['USER_RIGHTS']['CollAdmin'];
 		$sql = 'SELECT collid, collectionname FROM omcollections WHERE (collid IN('.implode(',',$collArr).')) ';
-		$collEditorArr = $GLOBALS['USER_RIGHTS']['CollEditor'];
-		if($collEditorArr){
-			$sql .= 'OR (collid IN('.implode(',',$collEditorArr).') AND colltype = "General Observations")';
+		if(isset($GLOBALS['USER_RIGHTS']['CollEditor'])){
+			$sql .= 'OR (collid IN('.implode(',',$GLOBALS['USER_RIGHTS']['CollEditor']).') AND colltype = "General Observations")';
 		}
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
diff --git a/collections/editor/includes/paleoinclude.php b/collections/editor/includes/paleoinclude.php
index 989fad1fbc..6ffbeb8faf 100644
--- a/collections/editor/includes/paleoinclude.php
+++ b/collections/editor/includes/paleoinclude.php
@@ -155,61 +155,57 @@ function setPaloParents(timePeriod){
 		<div id="earlyIntervalDiv">
 			<?php echo (defined('EARLYINTERVALLABEL')?EARLYINTERVALLABEL:'Early Interval'); ?>
 			<a href="#" onclick="return dwcDoc('earlyInterval')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="earlyInterval" onchange="earlyIntervalChanged(this)">
+			<select name="earlyinterval" onchange="earlyIntervalChanged(this)">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid){
-					echo '<option value="'.$term.'" '.(isset($occArr['earlyInterval']) && $occArr['earlyInterval']==$term?'SELECTED':'').'>'.$term.'</option>';
+					echo '<option value="'.$term.'" '.(isset($occArr['earlyinterval']) && $occArr['earlyinterval']==$term?'SELECTED':'').'>'.$term.'</option>';
 				}
 				?>
 			</select>
-			<!-- <input type="text" name="earlyInterval" value="<?php echo isset($occArr['earlyInterval'])?$occArr['earlyInterval']:''; ?>" onchange="fieldChanged('earlyInterval');" /> -->
 		</div>
 		<div id="lateIntervalDiv">
 			<?php echo (defined('LATEINTERVALLABEL')?LATEINTERVALLABEL:'Late Interval'); ?>
 			<a href="#" onclick="return dwcDoc('lateInterval')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="lateInterval" onchange="lateIntervalChanged(this)">
+			<select name="lateinterval" onchange="lateIntervalChanged(this)">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid){
-					echo '<option value="'.$term.'" '.(isset($occArr['lateInterval']) && $occArr['lateInterval']==$term?'SELECTED':'').'>'.$term.'</option>';
+					echo '<option value="'.$term.'" '.(isset($occArr['lateinterval']) && $occArr['lateinterval']==$term?'SELECTED':'').'>'.$term.'</option>';
 				}
 				?>
 			</select>
-			<!-- <input type="text" name="lateInterval" value="<?php echo isset($occArr['lateInterval'])?$occArr['lateInterval']:''; ?>" onchange="fieldChanged('lateInterval');" /> -->
 		</div>
 	</div>
 	<div style="clear:both">
 		<div id="absoluteAgeDiv">
 			<?php echo (defined('ABSOLUTEAGELABEL')?ABSOLUTEAGELABEL:'Absolute Age'); ?>
 			<a href="#" onclick="return dwcDoc('absoluteAge')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="absoluteAge" onchange="fieldChanged('absoluteAge');">
+			<select name="absoluteage" onchange="fieldChanged('absoluteage');">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid){
-					if($rankid == 60) echo '<option value="'.$term.'" '.(isset($occArr['absoluteAge']) && $occArr['absoluteAge']==$term?'SELECTED':'').'>'.$term.'</option>';
+					if($rankid == 60) echo '<option value="'.$term.'" '.(isset($occArr['absoluteage']) && $occArr['absoluteage']==$term?'SELECTED':'').'>'.$term.'</option>';
 				}
 				?>
 			</select>
-			<!-- <input type="text" name="absoluteAge" value="<?php echo isset($occArr['absoluteAge'])?$occArr['absoluteAge']:''; ?>" onchange="fieldChanged('absoluteAge');" /> -->
 		</div>
 		<div id="storageAgeDiv">
 			<?php echo (defined('STORAGEAGELABEL')?STORAGEAGELABEL:'Storage Age'); ?>
 			<a href="#" onclick="return dwcDoc('storageAge')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="storageAge" onchange="fieldChanged('storageAge');">
+			<select name="storageage" onchange="fieldChanged('storageage');">
 				<option value=""></option>
 				<?php
 				foreach($gtsTermArr as $term => $rankid){
-					if($rankid == 60) echo '<option value="'.$term.'" '.(isset($occArr['storageAge']) && $occArr['storageAge']==$term?'SELECTED':'').'>'.$term.'</option>';
+					if($rankid == 60) echo '<option value="'.$term.'" '.(isset($occArr['storageage']) && $occArr['storageage']==$term?'SELECTED':'').'>'.$term.'</option>';
 				}
 				?>
 			</select>
-			<!-- <input type="text" name="storageAge" value="<?php echo isset($occArr['storageAge'])?$occArr['storageAge']:''; ?>" onchange="fieldChanged('storageAge');" />  -->
 		</div>
 		<div id="localStageDiv">
 			<?php echo (defined('LOCALSTAGELABEL')?LOCALSTAGELABEL:'Local Stage'); ?>
 			<a href="#" onclick="return dwcDoc('localStage')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<input type="text" name="localStage" value="<?php echo isset($occArr['localStage'])?$occArr['localStage']:''; ?>" onchange="fieldChanged('localStage');" />
+			<input type="text" name="localstage" value="<?php echo isset($occArr['localstage'])?$occArr['localstage']:''; ?>" onchange="fieldChanged('localstage');" />
 		</div>
 	</div>
 	<div style="clear:both">
@@ -228,10 +224,10 @@ function setPaloParents(timePeriod){
 			<a href="#" onclick="return dwcDoc('taxonEnvironment')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<?php
 			$taxonEnvir = '';
-			if(isset($occArr['taxonEnvironment'])) $taxonEnvir = $occArr['taxonEnvironment'];
+			if(isset($occArr['taxonenvironment'])) $taxonEnvir = $occArr['taxonenvironment'];
 			?>
-			<select name="taxonEnvironment" onchange="fieldChanged('taxonEnvironment');">
-				<option value="">----------------</option>
+			<select name="taxonenvironment" onchange="fieldChanged('taxonenvironment');">
+				<option value=""></option>
 				<option <?php if($taxonEnvir=='marine') echo 'SELECTED'; ?>>marine</option>
 				<option<?php if($taxonEnvir=='non-marine') echo 'SELECTED'; ?>>non-marine</option>
 				<option<?php if($taxonEnvir=='marine and non-marine') echo 'SELECTED'; ?>>marine and non-marine</option>
@@ -251,7 +247,7 @@ function setPaloParents(timePeriod){
 		</div>
 		<div id="memberDiv">
 			<?php echo (defined('MEMBERLABEL')?MEMBERLABEL:'Member'); ?>
-			<a href="#" onclick="return dwcDoc('member')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<a href="#" onclick="return dwcDoc('member')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="member" value="<?php echo isset($occArr['member'])?$occArr['member']:''; ?>" onchange="fieldChanged('member');" />
 		</div>
 		<div id="lithologyDiv">
@@ -264,7 +260,7 @@ function setPaloParents(timePeriod){
 		<div id="stratRemarksDiv">
 			<?php echo (defined('TAXONENVIRONMENTLABEL')?TAXONENVIRONMENTLABEL:'Remarks'); ?>
 			<a href="#" onclick="return dwcDoc('stratRemarks')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<input type="text" name="stratRemarks" value="<?php echo isset($occArr['stratRemarks'])?$occArr['stratRemarks']:''; ?>" onchange="fieldChanged('stratRemarks');" />
+			<input type="text" name="stratremarks" value="<?php echo isset($occArr['stratremarks'])?$occArr['stratremarks']:''; ?>" onchange="fieldChanged('stratremarks');" />
 		</div>
 	</div>
 	<div style="clear:both">
@@ -276,7 +272,7 @@ function setPaloParents(timePeriod){
 		<div id="slidePropertiesDiv">
 			<?php echo (defined('SLIDEPROPERTIESLABEL')?SLIDEPROPERTIESLABEL:'Slide Properties'); ?>
 			<a href="#" onclick="return dwcDoc('slideProperties')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<input type="text" name="slideProperties" value="<?php echo isset($occArr['slideProperties'])?$occArr['slideProperties']:''; ?>" onchange="fieldChanged('slideProperties');" />
+			<input type="text" name="slideproperties" value="<?php echo isset($occArr['slideproperties'])?$occArr['slideproperties']:''; ?>" onchange="fieldChanged('slideproperties');" />
 		</div>
 	</div>
 </fieldset>
\ No newline at end of file

From 769ddf25ac10047395e83bbe221423254d1af366 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Tue, 10 Sep 2019 12:46:27 -0700
Subject: [PATCH 04/23] Paleo Development

- Moved control of display of custom modules into the control of the collections (e.g. omcollections)
- Added layout for adding a default editor customization to portal configuration file
- Removed omoccurlithostratigraphy field removed
---
 classes/OccurrenceEditorManager.php           | 11 ++--
 classes/OccurrenceIndividualManager.php       |  2 +-
 collections/editor/occurrenceeditor.php       |  2 +-
 collections/individual/index.php              | 55 +++++++++++--------
 .../dev/db_schema_patch_pending.sql           |  1 -
 .../schema-1.0/utf8/db_schema_patch-1.1.sql   |  4 ++
 config/symbini_template.php                   | 23 +++++++-
 css/occureditor.css                           |  2 -
 8 files changed, 66 insertions(+), 34 deletions(-)

diff --git a/classes/OccurrenceEditorManager.php b/classes/OccurrenceEditorManager.php
index ecb9528aed..a2dbbbd8d7 100644
--- a/classes/OccurrenceEditorManager.php
+++ b/classes/OccurrenceEditorManager.php
@@ -49,7 +49,7 @@ public function __construct($conn = null){
 			'labelproject','observeruid','basisofrecord','institutioncode','collectioncode','ownerinstitutioncode','datelastmodified', 'processingstatus',
 			'recordenteredby', 'dateentered');
 		$this->paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element','slideproperties');
+			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','element','slideproperties');
 	}
 
 	public function __destruct(){
@@ -89,14 +89,15 @@ private function setCollMap(){
 	}
 
 	public function getDynamicPropertiesArr(){
+		global $EDITOR_PROPERTIES;
 		$propArr = array();
+		if(isset($EDITOR_PROPERTIES)) $propArr = $EDITOR_PROPERTIES;
 		$dynPropArr = array();
 		if(array_key_exists('dynamicproperties', $this->collMap)){
 			$dynPropArr = json_decode($this->collMap['dynamicproperties'],true);
-			if(isset($dynPropArr['editorProp'])) $propArr = $dynPropArr['editorProp'];
+			if(isset($dynPropArr['editorProps'])) $propArr = array_merge($propArr,$dynPropArr['editorProps']);
 		}
-		$dynPropArr = array("editorProp"=>array("paleoMod"=>1,"catalogDupeCheck"=>1));
-		if(isset($dynPropArr['editorProp'])) $propArr = $dynPropArr['editorProp'];
+		//$dynPropArr = array("editorProp"=>array("paleoMod"=>1,"catalogDupeCheck"=>1));
 		return $propArr;
 	}
 
@@ -1625,7 +1626,7 @@ public function carryOverValues($fArr){
 			'minimumelevationinmeters','maximumelevationinmeters','verbatimelevation','minimumdepthinmeters','maximumdepthinmeters','verbatimdepth',
 			'habitat','substrate','lifestage', 'sex', 'individualcount', 'samplingprotocol', 'preparations',
 			'associatedtaxa','basisofrecord','language','labelproject','eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','lithdescription','element');
+			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','element');
 		$retArr = $this->cleanOutArr(array_intersect_key($fArr,array_flip($locArr)));
 		return $retArr;
 	}
diff --git a/classes/OccurrenceIndividualManager.php b/classes/OccurrenceIndividualManager.php
index b865b2a254..430ddde545 100644
--- a/classes/OccurrenceIndividualManager.php
+++ b/classes/OccurrenceIndividualManager.php
@@ -220,7 +220,7 @@ private function loadImages(){
 
 	private function loadPaleo(){
 		$sql = 'SELECT paleoid, eon, era, period, epoch, earlyinterval, lateinterval, absoluteage, storageage, stage, localstage, biota, '.
-			'biostratigraphy, lithogroup, formation, taxonenvironment, member, lithology, stratremarks, lithdescription, element, slideproperties '.
+			'biostratigraphy, lithogroup, formation, taxonenvironment, member, lithology, stratremarks, element, slideproperties '.
 			'FROM omoccurpaleo WHERE occid = '.$this->occid;
 		$rs = $this->conn->query($sql);
 		if($rs){
diff --git a/collections/editor/occurrenceeditor.php b/collections/editor/occurrenceeditor.php
index 00d1a9b609..3f296080ea 100644
--- a/collections/editor/occurrenceeditor.php
+++ b/collections/editor/occurrenceeditor.php
@@ -1133,7 +1133,7 @@ function requestImage(){
 											</div>
 										</fieldset>
 										<?php
-										if(isset($editorPropArr['paleoMod']) && $editorPropArr['paleoMod']) include('includes/paleoinclude.php');
+										if(isset($editorPropArr['modules-panel']['paleo']['status']) && $editorPropArr['modules-panel']['paleo']['status']) include('includes/paleoinclude.php');
 										?>
 										<fieldset>
 											<legend><b>Misc</b></legend>
diff --git a/collections/individual/index.php b/collections/individual/index.php
index 45983a510e..826c5c9f0f 100644
--- a/collections/individual/index.php
+++ b/collections/individual/index.php
@@ -765,30 +765,39 @@ function initializeMap(){
 							<div style="clear:both;">
 								<b>Paleontology terms: </b>
 								<?php
-								$paleoStr = '';
-								if($occArr['eon']) $paleoStr .= '; '.$occArr['eon'];
-								if($occArr['era']) $paleoStr .= '; '.$occArr['era'];
-								if($occArr['period']) $paleoStr .= '; '.$occArr['period'];
-								if($occArr['epoch']) $paleoStr .= '; '.$occArr['epoch'];
-								if($occArr['earlyinterval']) $paleoStr .= '; '.$occArr['earlyinterval'];
-								if($occArr['lateinterval']) $paleoStr .= ' to '.$occArr['lateinterval'];
-								if($occArr['absoluteage']) $paleoStr .= '; <b>absolute age:</b> '.$occArr['absoluteage'];
-								if($occArr['storageage']) $paleoStr .= '; <b>storage age:</b> '.$occArr['storageage'];
-								if($occArr['stage']) $paleoStr .= '; <b>stage:</b> '.$occArr['stage'];
-								if($occArr['localstage']) $paleoStr .= '; <b>local stage:</b> '.$occArr['localstage'];
-								if($occArr['biota']) $paleoStr .= '; <b>biota:</b> '.$occArr['biota'];
-								if($occArr['biostratigraphy']) $paleoStr .= '; <b>biostratigraphy:</b> '.$occArr['biostratigraphy'];
-								if($occArr['lithogroup']) $paleoStr .= '; <b>group:</b> '.$occArr['lithogroup'];
-								if($occArr['formation']) $paleoStr .= '; <b>formation:</b> '.$occArr['formation'];
-								if($occArr['taxonenvironment']) $paleoStr .= '; <b>Taxon Environment:</b> '.$occArr['taxonenvironment'];
-								if($occArr['member']) $paleoStr .= '; <b>member:</b> '.$occArr['member'];
-								if($occArr['lithology']) $paleoStr .= '; <b>lithology:</b> '.$occArr['lithology'];
-								if($occArr['stratremarks']) $paleoStr .= '; <b>remarks:</b> '.$occArr['stratremarks'];
-								if($occArr['lithdescription']) $paleoStr .= '; <b>lith description:</b> '.$occArr['lithdescription'];
-								if($occArr['element']) $paleoStr .= '; <b>element:</b> '.$occArr['element'];
-								if($occArr['slideproperties']) $paleoStr .= '; <b>slide properties:</b> '.$occArr['slideproperties'];
-								echo trim($paleoStr,'; ');
+								$paleoStr1 = '';
+								if($occArr['eon']) $paleoStr1 .= '; '.$occArr['eon'];
+								if($occArr['era']) $paleoStr1 .= '; '.$occArr['era'];
+								if($occArr['period']) $paleoStr1 .= '; '.$occArr['period'];
+								if($occArr['epoch']) $paleoStr1 .= '; '.$occArr['epoch'];
+								if($occArr['stage']) $paleoStr1 .= '; '.$occArr['stage'];
+								if($occArr['earlyinterval']) $paleoStr1 .= '; '.$occArr['earlyinterval'];
+								if($occArr['lateinterval']) $paleoStr1 .= ' to '.$occArr['lateinterval'];
+								if($paleoStr1) echo trim($paleoStr1,'; ');
 								?>
+								<div style="margin-left:10px">
+									<?php
+									$paleoStr2 = '';
+									if($occArr['absoluteage']) $paleoStr2 .= '; <b>absolute age:</b> '.$occArr['absoluteage'];
+									if($occArr['storageage']) $paleoStr2 .= '; <b>storage age:</b> '.$occArr['storageage'];
+									if($occArr['localstage']) $paleoStr2 .= '; <b>local stage:</b> '.$occArr['localstage'];
+									if($occArr['biota']) $paleoStr2 .= '; <b>biota:</b> '.$occArr['biota'];
+									if($occArr['biostratigraphy']) $paleoStr2 .= '; <b>biostratigraphy:</b> '.$occArr['biostratigraphy'];
+									if($paleoStr2) echo '<div>'.trim($paleoStr2,'; ').'<div>';
+									$paleoStr3 = '';
+									if($occArr['lithogroup']) $paleoStr3 .= '; <b>group:</b> '.$occArr['lithogroup'];
+									if($occArr['formation']) $paleoStr3 .= '; <b>formation:</b> '.$occArr['formation'];
+									if($occArr['taxonenvironment']) $paleoStr3 .= '; <b>taxon environment:</b> '.$occArr['taxonenvironment'];
+									if($occArr['member']) $paleoStr3 .= '; <b>member:</b> '.$occArr['member'];
+									if($occArr['lithology']) $paleoStr3 .= '; <b>lithology:</b> '.$occArr['lithology'];
+									if($paleoStr3) echo '<div>'.trim($paleoStr3,'; ').'</div>';
+									if($occArr['stratremarks']) echo '<div><b>remarks:</b> '.$occArr['stratremarks'].'</div>';
+									$paleoStr4 = '';
+									if($occArr['element']) $paleoStr4 .= '; <b>element:</b> '.$occArr['element'];
+									if($occArr['slideproperties']) $paleoStr4 .= '; <b>slide properties:</b> '.$occArr['slideproperties'];
+									if($paleoStr4) echo '<div>'.trim($paleoStr4,'; ').'</div>';
+									?>
+								</div>
 							</div>
 							<?php
 						}
diff --git a/config/schema-1.0/dev/db_schema_patch_pending.sql b/config/schema-1.0/dev/db_schema_patch_pending.sql
index acdfeac583..3e65c6559b 100644
--- a/config/schema-1.0/dev/db_schema_patch_pending.sql
+++ b/config/schema-1.0/dev/db_schema_patch_pending.sql
@@ -82,7 +82,6 @@ CREATE TABLE `omoccurpaleo` (
   `member` VARCHAR(65) NULL,
   `lithology` VARCHAR(65) NULL,
   `stratRemarks` VARCHAR(250) NULL,
-  `lithDescription` VARCHAR(250) NULL,
   `element` VARCHAR(250) NULL,
   `slideProperties` VARCHAR(1000) NULL,
   `initialtimestamp` TIMESTAMP NULL DEFAULT current_timestamp,
diff --git a/config/schema-1.0/utf8/db_schema_patch-1.1.sql b/config/schema-1.0/utf8/db_schema_patch-1.1.sql
index 69a3b55ff4..a7ad69b5c8 100644
--- a/config/schema-1.0/utf8/db_schema_patch-1.1.sql
+++ b/config/schema-1.0/utf8/db_schema_patch-1.1.sql
@@ -895,6 +895,10 @@ CREATE TABLE `omoccurlithostratigraphy` (
   CONSTRAINT `FK_occurlitho_occid` FOREIGN KEY (`occid`) REFERENCES `omoccurrences` (`occid`) ON DELETE CASCADE  ON UPDATE CASCADE
 );
 
+DROP TABLE omoccurlithostratigraphy;
+DROP TABLE paleochronostratigraphy;
+
+
 CREATE TABLE `useraccesstokens` (
   `tokid` int(11) NOT NULL AUTO_INCREMENT,
   `uid` int unsigned NOT NULL,
diff --git a/config/symbini_template.php b/config/symbini_template.php
index 96e013a419..f05156af2d 100644
--- a/config/symbini_template.php
+++ b/config/symbini_template.php
@@ -63,10 +63,31 @@
 	'CC BY (Attribution)' => 'http://creativecommons.org/licenses/by/4.0/',
 	'CC BY-NC (Attribution-Non-Commercial)' => 'http://creativecommons.org/licenses/by-nc/4.0/'
 );
-//$PROCESSINGSTATUS = array('unprocessed','unprocessed/NLP','stage 1','stage 2','stage 3','pending review-nfn','pending review','expert required','reviewed','closed');
 
 $CSS_VERSION_LOCAL = '20170414';		//Changing this variable will force a refresh of main.css styles within users browser cache for all pages
 
+/*
+//Default editor properties; properties defined in collection will override these values
+$EDITOR_PROPERTIES = array(
+	'modules-panel' => array(
+		'paleo' => array('status'=>0,'titleOverride'=>'Paleonotology Terms')
+	),
+	'features' => array('catalogDupeCheck'=>1,'otherCatNumDupeCheck'=>0,'dupeSearch'=>1),
+	'labelOverrides' => array(),
+	'cssTerms' => array(
+		'#recordNumberDiv'=>array('float'=>'left','margin-right'=>'2px'),
+		'#recordNumberDiv input'=>array('width'=>'60px'),
+		'#eventDateDiv'=>array('float'=>'left'),
+		'#eventDateDiv input'=>array('width'=>'110px')
+	),
+	'customCSS' => array(),
+	'customLookups' => array(
+		'processingStatus' => array('Unprocessed','Stage 1','Stage 2','Pending Review','Expert Required','Reviewed','Closed')
+	)
+);
+// json: {"editorProps":{"modules-panel":{"paleo":{"status":1}}}}
+*/
+
 
 //Base code shared by all pages; leave as is
 include_once("symbbase.php");
diff --git a/css/occureditor.css b/css/occureditor.css
index 709779275b..42e18f7cd4 100644
--- a/css/occureditor.css
+++ b/css/occureditor.css
@@ -820,8 +820,6 @@ body{
 #lithologyDiv{ float:left; margin:3px; }
 #stratRemarksDiv{ float:left; margin:3px; }
 #stratRemarksDiv input{ width:600px; }
-#lithDescriptionDiv{ float:left; margin:3px; }
-#lithDescriptionDiv input{ width:600px }
 #elementDiv{ float:left; margin:3px; }
 #slidePropertiesDiv{ float:left; margin:3px; }
 #slidePropertiesDiv input{ width:400px; }

From 9d9ff781e9d9bb9434704d5e9ba35dc6b5d70cc6 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Tue, 10 Sep 2019 12:53:41 -0700
Subject: [PATCH 05/23] Paleo Adjustment

- Minor error resolve
---
 config/schema-1.0/dev/db_schema_patch_pending.sql | 3 +++
 config/schema-1.0/utf8/db_schema_patch-1.1.sql    | 3 ---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/config/schema-1.0/dev/db_schema_patch_pending.sql b/config/schema-1.0/dev/db_schema_patch_pending.sql
index 3e65c6559b..23fef85d7e 100644
--- a/config/schema-1.0/dev/db_schema_patch_pending.sql
+++ b/config/schema-1.0/dev/db_schema_patch_pending.sql
@@ -119,6 +119,9 @@ INSERT INTO omoccurpaleogts(gtsterm,rankid,rankname,parentgtsid)
 INSERT INTO omoccurpaleogts(gtsterm,rankid,rankname,parentgtsid)
   SELECT DISTINCT p.stage, 60, "age", g.gtsid FROM paleochronostratigraphy p INNER JOIN omoccurpaleogts g ON p.epoch = g.gtsterm WHERE stage IS NOT NULL;
 
+DROP TABLE omoccurlithostratigraphy;
+DROP TABLE paleochronostratigraphy;
+
 
 ALTER TABLE `images` 
   ADD INDEX `Index_images_datelastmod` (`InitialTimeStamp` ASC);
diff --git a/config/schema-1.0/utf8/db_schema_patch-1.1.sql b/config/schema-1.0/utf8/db_schema_patch-1.1.sql
index a7ad69b5c8..270ead24a5 100644
--- a/config/schema-1.0/utf8/db_schema_patch-1.1.sql
+++ b/config/schema-1.0/utf8/db_schema_patch-1.1.sql
@@ -895,9 +895,6 @@ CREATE TABLE `omoccurlithostratigraphy` (
   CONSTRAINT `FK_occurlitho_occid` FOREIGN KEY (`occid`) REFERENCES `omoccurrences` (`occid`) ON DELETE CASCADE  ON UPDATE CASCADE
 );
 
-DROP TABLE omoccurlithostratigraphy;
-DROP TABLE paleochronostratigraphy;
-
 
 CREATE TABLE `useraccesstokens` (
   `tokid` int(11) NOT NULL AUTO_INCREMENT,

From 0fd389625450604829c8d8e2c1ac802379f5750d Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Thu, 12 Sep 2019 14:50:19 -0700
Subject: [PATCH 06/23] Occurrence Duplicate display bug

- Don't display thumbnail or image link for protected specimens, unless user is logged in and with access permissions
- Scientific Author failing to display within duplicate display tab
---
 classes/OccurrenceDuplicate.php  |  6 +++---
 collections/individual/index.php | 28 +++++++++++++++-------------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/classes/OccurrenceDuplicate.php b/classes/OccurrenceDuplicate.php
index 55dba96923..dfd5be810f 100644
--- a/classes/OccurrenceDuplicate.php
+++ b/classes/OccurrenceDuplicate.php
@@ -30,7 +30,7 @@ public function getClusterArr($occid){
 				$retArr[$r1->duplicateid]['description'] = $r1->description;
 				$retArr[$r1->duplicateid]['notes'] = $r1->notes;
 			}
-			$rs1->close();
+			$rs1->free();
 		}
 		else{
 			$this->errorStr = 'ERROR getting list of duplicate records [1]: '.$this->conn->error;
@@ -39,7 +39,7 @@ public function getClusterArr($occid){
 
 		if($retArr){
 			$sql = 'SELECT d.duplicateid, d.occid, c.institutioncode, c.collectioncode, c.collectionname, o.catalognumber, '.
-				'o.occurrenceid, o.sciname, o.identifiedby, o.dateidentified, '.
+				'o.occurrenceid, o.sciname, o.scientificnameauthorship, o.identifiedby, o.dateidentified, '.
 				'o.recordedby, o.recordnumber, o.eventdate, d.notes, i.url, i.thumbnailurl '.
 				'FROM omoccurduplicatelink d INNER JOIN omoccurrences o ON d.occid = o.occid '.
 				'INNER JOIN omcollections c ON o.collid = c.collid '.
@@ -48,7 +48,7 @@ public function getClusterArr($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,
+							'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' => $r->url);
diff --git a/collections/individual/index.php b/collections/individual/index.php
index 826c5c9f0f..139525837f 100644
--- a/collections/individual/index.php
+++ b/collections/individual/index.php
@@ -968,7 +968,7 @@ function initializeMap(){
 							if($occArr['catalognumber']) echo '<div><b>Catalog Number:</b> '.$occArr['catalognumber'].'</div>';
 							if($occArr['occurrenceid']) echo '<div><b>GUID:</b> '.$occArr['occurrenceid'].'</div>';
 							echo '<div><b>Latest Identification:</b> ';
-							if($securityCode < 2) echo '<i>'.$occArr['sciname'].'</i> '.$occArr['author'];
+							if($securityCode < 2) echo '<i>'.$occArr['sciname'].'</i> '.$occArr['scientificnameauthorship'];
 							else echo '<b>species identification protected</b>';
 							echo '</div>';
 							if($occArr['identifiedby']) echo '<div><b>Identified by:</b> '.$occArr['identifiedby'].'<span stlye="margin-left:30px;">'.$occArr['dateidentified'].'</span></div>';
@@ -993,19 +993,21 @@ function initializeMap(){
 										if($dupArr['notes']) echo '<div>'.$dupArr['notes'].'</div>';
 										echo '<div><a href="#" onclick="openIndividual('.$dupOccid.')">Show Full Details</a></div>';
 										echo '</div>';
-										if($dupArr['url']){
-											$url = $dupArr['url'];
-											$tnUrl = $dupArr['tnurl'];
-											if(!$tnUrl) $tnUrl = $url;
-											if($IMAGE_DOMAIN){
-												if(substr($url,0,1) == '/') $url = $IMAGE_DOMAIN.$url;
-												if(substr($tnUrl,0,1) == '/') $tnUrl = $IMAGE_DOMAIN.$tnUrl;
+										if(!$securityCode){
+											if($dupArr['url']){
+												$url = $dupArr['url'];
+												$tnUrl = $dupArr['tnurl'];
+												if(!$tnUrl) $tnUrl = $url;
+												if($IMAGE_DOMAIN){
+													if(substr($url,0,1) == '/') $url = $IMAGE_DOMAIN.$url;
+													if(substr($tnUrl,0,1) == '/') $tnUrl = $IMAGE_DOMAIN.$tnUrl;
+												}
+												echo '<div style="float:left;margin:10px;">';
+												echo '<a href="'.$url.'">';
+												echo '<img src="'.$tnUrl.'" style="width:100px;border:1px solid grey" />';
+												echo '</a>';
+												echo '</div>';
 											}
-											echo '<div style="float:left;margin:10px;">';
-											echo '<a href="'.$url.'">';
-											echo '<img src="'.$tnUrl.'" style="width:100px;border:1px solid grey" />';
-											echo '</a>';
-											echo '</div>';
 										}
 										echo '<div style="margin:10px 0px;clear:both"><hr/></div>';
 										echo '</div>';

From 81914edc406ff4155507f331933820be68a1121f Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Thu, 12 Sep 2019 17:23:02 -0700
Subject: [PATCH 07/23] Occurrence Editor bug

- Resolve issue causing page to fail when omoccurpaleo table has not yet been created
---
 classes/OccurrenceEditorManager.php | 72 ++++++++++++++++-------------
 1 file changed, 41 insertions(+), 31 deletions(-)

diff --git a/classes/OccurrenceEditorManager.php b/classes/OccurrenceEditorManager.php
index a2dbbbd8d7..37944b91f3 100644
--- a/classes/OccurrenceEditorManager.php
+++ b/classes/OccurrenceEditorManager.php
@@ -26,6 +26,8 @@ class OccurrenceEditorManager {
 	protected $errorArr = array();
 	protected $isShareConn = false;
 
+	private $paleoActivated = false;
+
 	public function __construct($conn = null){
 		if($conn){
 			$this->conn = $conn;
@@ -97,7 +99,7 @@ public function getDynamicPropertiesArr(){
 			$dynPropArr = json_decode($this->collMap['dynamicproperties'],true);
 			if(isset($dynPropArr['editorProps'])) $propArr = array_merge($propArr,$dynPropArr['editorProps']);
 		}
-		//$dynPropArr = array("editorProp"=>array("paleoMod"=>1,"catalogDupeCheck"=>1));
+		if(isset($propArr['modules-panel']['paleo']['status']) && $propArr['modules-panel']['paleo']['status']) $this->paleoActivated = true;
 		return $propArr;
 	}
 
@@ -802,7 +804,7 @@ public function editOccurrence($occArr, $editorStatus){
 						(in_array('recordenteredby',$editArr)?'':',recordenteredby').
 						' FROM omoccurrences o ';
 					}
-					if(array_intersect($editArr, $this->paleoFieldArr)){
+					if($this->paleoActivated && array_intersect($editArr, $this->paleoFieldArr)){
 						$sql .= 'LEFT JOIN omoccurpaleo p ON o.occid = p.occid ';
 					}
 					$sql .= 'WHERE o.occid = '.$occArr['occid'];
@@ -913,7 +915,7 @@ public function editOccurrence($occArr, $editorStatus){
 							}
 						}
 						//Deal with paleo fields
-						if(array_key_exists('eon',$occArr)){
+						if($this->paleoActivated && array_key_exists('eon',$occArr)){
 							//Check to see if paleo record already exists
 							$paleoRecordExist = false;
 							$paleoSql = 'SELECT paleoid FROM omoccurpaleo WHERE occid = '.$occArr['occid'];
@@ -1085,7 +1087,7 @@ public function addOccurrence($occArr){
 					$status .= '(WARNING: Symbiota GUID mapping failed) ';
 				}
 				//Deal with paleo
-				if(array_key_exists('eon',$occArr)){
+				if($this->paleoActivated && array_key_exists('eon',$occArr)){
 					//Add new record
 					$paleoFrag1 = '';
 					$paleoFrag2 = '';
@@ -1234,17 +1236,19 @@ public function deleteOccurrence($delOccid){
 				}
 
 				//Archive paleo
-				$sql = 'SELECT * FROM omoccurpaleo WHERE occid = '.$delOccid;
-				$rs = $this->conn->query($sql);
-				if($rs){
-					$paleoArr = array();
-					if($r = $rs->fetch_assoc()){
-						foreach($r as $k => $v){
-							if($v) $paleoArr[$k] = $this->encodeStrTargeted($v,$CHARSET,'utf8');
+				if($this->paleoActivated){
+					$sql = 'SELECT * FROM omoccurpaleo WHERE occid = '.$delOccid;
+					$rs = $this->conn->query($sql);
+					if($rs){
+						$paleoArr = array();
+						if($r = $rs->fetch_assoc()){
+							foreach($r as $k => $v){
+								if($v) $paleoArr[$k] = $this->encodeStrTargeted($v,$CHARSET,'utf8');
+							}
 						}
+						$rs->free();
+						$archiveArr['paleo'] = $paleoArr;
 					}
-					$rs->free();
-					$archiveArr['paleo'] = $paleoArr;
 				}
 
 				//Archive Exsiccati info
@@ -1348,10 +1352,12 @@ public function mergeRecords($targetOccid,$sourceOccid){
 		}
 
 		//Remap paleo
-		$sql = 'UPDATE omoccurpaleo SET occid = '.$targetOccid.' WHERE occid = '.$sourceOccid;
-		if(!$this->conn->query($sql)){
-			//$this->errorArr[] .= '; ERROR remapping paleos: '.$this->conn->error;
-			//$status = false;
+		if($this->paleoActivated){
+			$sql = 'UPDATE omoccurpaleo SET occid = '.$targetOccid.' WHERE occid = '.$sourceOccid;
+			if(!$this->conn->query($sql)){
+				//$this->errorArr[] .= '; ERROR remapping paleos: '.$this->conn->error;
+				//$status = false;
+			}
 		}
 
 		//Delete source occurrence edits
@@ -1472,15 +1478,17 @@ private function setLoanData(){
 	}
 
 	private function setPaleoData(){
-		$sql = 'SELECT '.implode(',',$this->paleoFieldArr).' FROM omoccurpaleo WHERE occid = '.$this->occid;
-		//echo $sql;
-		$rs = $this->conn->query($sql);
-		if($r = $rs->fetch_assoc()){
-			foreach($this->paleoFieldArr as $term){
-				$this->occurrenceMap[$this->occid][$term] = $r[$term];
+		if($this->paleoActivated){
+			$sql = 'SELECT '.implode(',',$this->paleoFieldArr).' FROM omoccurpaleo WHERE occid = '.$this->occid;
+			//echo $sql;
+			$rs = $this->conn->query($sql);
+			if($r = $rs->fetch_assoc()){
+				foreach($this->paleoFieldArr as $term){
+					$this->occurrenceMap[$this->occid][$term] = $r[$term];
+				}
 			}
+			$rs->free();
 		}
-		$rs->free();
 	}
 
 	private function setExsiccati(){
@@ -1570,7 +1578,7 @@ public function batchUpdateField($fieldName,$oldValue,$newValue,$buMatch){
 					$statusStr = 'ERROR adding update to omoccuredits: '.$this->conn->error;
 				}
 				//Apply edits to core tables
-				if(array_key_exists($fn, $this->paleoFieldArr)){
+				if($this->paleoActivated && array_key_exists($fn, $this->paleoFieldArr)){
 					$sql = 'UPDATE omoccurpaleo SET '.$fn.' = '.$nvSqlFrag.' '.$sqlWhere;
 				}
 				else{
@@ -2118,13 +2126,15 @@ public function getCollectionList(){
 
 	public function getPaleoGtsTerms(){
 		$retArr = array();
-		$sql = 'SELECT gtsterm, rankid FROM omoccurpaleogts ';
-		$rs = $this->conn->query($sql);
-		while($r = $rs->fetch_object()){
-			$retArr[$r->gtsterm] = $r->rankid;
+		if($this->paleoActivated){
+			$sql = 'SELECT gtsterm, rankid FROM omoccurpaleogts ';
+			$rs = $this->conn->query($sql);
+			while($r = $rs->fetch_object()){
+				$retArr[$r->gtsterm] = $r->rankid;
+			}
+			$rs->free();
+			ksort($retArr);
 		}
-		$rs->free();
-		ksort($retArr);
 		return $retArr;
 	}
 

From efd7aa68712e8d3fea8398403cf14866a5046a96 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Mon, 16 Sep 2019 13:25:24 -0700
Subject: [PATCH 08/23] Bug: parse error

---
 classes/OccurrenceEditorServices.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/classes/OccurrenceEditorServices.php b/classes/OccurrenceEditorServices.php
index 8813387fce..41b870f934 100644
--- a/classes/OccurrenceEditorServices.php
+++ b/classes/OccurrenceEditorServices.php
@@ -39,7 +39,7 @@ public function getPaleoGtsParents($term){
 					$parentId = 0;
 				}
 				else{
-					$retArr[] = array("rankid" => [$r->rankid], "value" => $r->gtsterm);
+					$retArr[] = array("rankid" => $r->rankid, "value" => $r->gtsterm);
 					$parentId = $r->parentgtsid;
 				}
 			}

From 5eef47791f52c7c1093f7c21cccfd22c85ba1801 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Mon, 16 Sep 2019 15:31:09 -0700
Subject: [PATCH 09/23] Occurrence Search Minor bug

- Form will now accept submissions even if only polygon is added into search form
---
 js/symb/collections.harvestparams.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/js/symb/collections.harvestparams.js b/js/symb/collections.harvestparams.js
index 6d86e6ad2b..6878679c1f 100644
--- a/js/symb/collections.harvestparams.js
+++ b/js/symb/collections.harvestparams.js
@@ -14,7 +14,7 @@ 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.pointlat.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)){
 		alert("Please fill in at least one search parameter!");

From b961e235b73a204f415aa23e0be28495096e5671 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Mon, 16 Sep 2019 20:58:26 -0700
Subject: [PATCH 10/23] Collection Listing and Menu Adjustments

- Misc adjustments to layout
- Adjustments to collection name, code, and icon display
- Added language support
---
 classes/OccurrenceCollectionProfile.php       | 11 ++----
 classes/OccurrenceSearchSupport.php           | 10 ++---
 collections/individual/index.php              | 39 +++++++++----------
 collections/misc/collprofiles.php             | 26 ++++++-------
 .../lang/collections/misc/collprofiles.en.php | 19 ++++++++-
 .../lang/collections/misc/collprofiles.es.php | 19 ++++++++-
 css/base.css                                  |  1 +
 7 files changed, 77 insertions(+), 48 deletions(-)

diff --git a/classes/OccurrenceCollectionProfile.php b/classes/OccurrenceCollectionProfile.php
index bced4ec329..1520760782 100644
--- a/classes/OccurrenceCollectionProfile.php
+++ b/classes/OccurrenceCollectionProfile.php
@@ -135,14 +135,14 @@ public function getMetadataHtml($collArr, $LANG){
 		$outStr .= '<div style="margin-top:5px;">';
 		$outStr .= '<b>'.$LANG['MANAGEMENT'].':</b> ';
 		if($collArr['managementtype'] == 'Live Data'){
-			$outStr .= 'Live Data managed directly within data portal';
+			$outStr .= (isset($LANG['LIVE_DATA'])?$LANG['LIVE_DATA']:'Live Data managed directly within data portal');
 		}
 		else{
 			if($collArr['managementtype'] == 'Aggregate'){
-				$outStr .= 'Data harvested from a data aggregator';
+				$outStr .= (isset($LANG['DATA_AGGREGATE'])?$LANG['DATA_AGGREGATE']:'Data harvested from a data aggregator');
 			}
 			else{
-				$outStr .= 'Data snapshot of local collection database ';
+				$outStr .= (isset($LANG['DATA_SNAPSHOT'])?$LANG['DATA_SNAPSHOT']:'Data snapshot of local collection database ');
 			}
 			$outStr .= '<div style="margin-top:5px;"><b>'.$LANG['LAST_UPDATE'].':</b> '.$collArr['uploaddate'].'</div>';
 		}
@@ -165,9 +165,6 @@ public function getMetadataHtml($collArr, $LANG){
 			if($GLOBALS['SYMB_UID']){
 				$outStr .= '<a href="../../webservices/dwc/dwcapubhandler.php?collid='.$collArr['collid'].'">'.(isset($LANG['FULL_DATA'])?$LANG['FULL_DATA']:'DwC-Archive File').'</a>';
 			}
-			else{
-				$outStr .= '<a href="../../profile/index.php?refurl=../collections/misc/collprofiles.php?collid='.$collArr['collid'].'">'.(isset($LANG['LOGIN_TO_ACCESS'])?$LANG['LOGIN_TO_ACCESS']:'Login for access').'</a>';
-			}
 		}
 		elseif($collArr['managementtype'] == 'Snapshot'){
 			$pathArr = $this->getDwcaPath($collArr['collid']);
@@ -201,7 +198,7 @@ public function getMetadataHtml($collArr, $LANG){
 			if($rightsUrl) $outStr .= '</a>';
 		}
 		elseif(file_exists('../../misc/usagepolicy.php')){
-			$outStr .= '<a href="../../misc/usagepolicy.php" target="_blank">Usage policy</a>';
+			$outStr .= '<a href="../../misc/usagepolicy.php" target="_blank">'.(isset($LANG['USAGE_POLICY'])?$LANG['USAGE_POLICY']:'Usage policy').'</a>';
 		}
 		$outStr .= '</div>';
 		if($collArr['rightsholder']){
diff --git a/classes/OccurrenceSearchSupport.php b/classes/OccurrenceSearchSupport.php
index 5a8ce3410f..c1a1ded716 100644
--- a/classes/OccurrenceSearchSupport.php
+++ b/classes/OccurrenceSearchSupport.php
@@ -118,7 +118,7 @@ public function outputFullCollArr($collGrpArr, $targetCatID = '', $displayIcons
 						<?php
 						if($displayIcons){
 							?>
-							<td style="<?php echo ($catIcon?'width:40px':''); ?>">
+							<td style="<?php echo ($catIcon?'width:40px;height:35px;':''); ?>">
 								<?php
 								if($catIcon){
 									$catIcon = (substr($catIcon,0,6)=='images'?$CLIENT_ROOT:'').$catIcon;
@@ -164,7 +164,7 @@ public function outputFullCollArr($collGrpArr, $targetCatID = '', $displayIcons
 											<?php
 											if($displayIcons){
 												?>
-												<td style="width:40px;">
+												<td style="width:40px;height:35px">
 													<?php
 													if($collName2["icon"]){
 														$cIcon = (substr($collName2["icon"],0,6)=='images'?$CLIENT_ROOT:'').$collName2["icon"];
@@ -177,7 +177,7 @@ public function outputFullCollArr($collGrpArr, $targetCatID = '', $displayIcons
 												<?php
 											}
 											?>
-											<td style="width:25px;">
+											<td style="width:25px;padding-top:8px;">
 												<?php
 												echo '<input data-role="none" name="db[]" value="'.$collid.'" type="checkbox" class="cat-'.$idStr.'" onclick="unselectCat(\'cat-'.$idStr.'-Input\')" '.($catSelected || !$collSelArr || in_array($collid, $collSelArr)?'checked':'').' />';
 												?>
@@ -222,7 +222,7 @@ public function outputFullCollArr($collGrpArr, $targetCatID = '', $displayIcons
 						<?php
 						if($displayIcons){
 							?>
-							<td style="<?php ($cArr["icon"]?'width:35px':''); ?>">
+							<td style="<?php ($cArr["icon"]?'width:40px;height:35px':''); ?>">
 								<?php
 								if($cArr["icon"]){
 									$cIcon = (substr($cArr["icon"],0,6)=='images'?$CLIENT_ROOT:'').$cArr["icon"];
@@ -236,7 +236,7 @@ public function outputFullCollArr($collGrpArr, $targetCatID = '', $displayIcons
 							<?php
 						}
 						?>
-						<td style="width:25px;">
+						<td style="width:25px;padding-top:8px;">
 							<?php
 							echo '<input data-role="none" name="db[]" value="'.$collid.'" type="checkbox" onclick="uncheckAll()" '.(!$collSelArr || in_array($collid, $collSelArr)?'checked':'').' />';
 							?>
diff --git a/collections/individual/index.php b/collections/individual/index.php
index 139525837f..1f8eaa69a7 100644
--- a/collections/individual/index.php
+++ b/collections/individual/index.php
@@ -336,33 +336,30 @@ function initializeMap(){
 					</div>
 					<?php
 					$iconUrl = (substr($collMetadata["icon"],0,6)=='images'?'../../':'').$collMetadata['icon'];
-					if($iconUrl) $iconUrl = '<img border="1" height="50" width="50" src="'.$iconUrl.'" /><br/>';
-					$instCode = $collMetadata['institutioncode'];
-					if(isset($collMetadata['collectioncode'])){
-						$instCode .= (strlen($collMetadata['institutioncode'])<7?' : ':'<br/>').$collMetadata['collectioncode'];
-					}
-					elseif(!isset($occArr['secondaryinstcode']) && isset($occArr['secondarycollcode'])){
-						$instCode .= (strlen($collMetadata['institutioncode'])<7?' : ':'<br/>').$occArr['secondarycollcode'];
-					}
-					if($occArr['secondaryinstcode']){
-						$instCode .= '<div>';
-						$instCode .= $occArr['secondaryinstcode'];
-						if(isset($occArr['secondarycollcode'])){
-							$instCode .= (strlen($occArr['secondaryinstcode'])<7?' : ':'<br/>');
-							$instCode .= $occArr['secondarycollcode'];
-						}
-						$instCode .= '</div>';
-					}
 					if($iconUrl){
+						$iconUrl = '<img border="1" height="50" width="50" src="'.$iconUrl.'" />';
 						echo '<div style="float:left;margin:15px 0px;text-align:center;font-weight:bold;width:120px;">';
 						echo $iconUrl;
 						echo '</div>';
 					}
+					$instCode = $collMetadata['institutioncode'];
+					if(isset($collMetadata['collectioncode']) && $collMetadata['collectioncode']){
+						$instCode .= ':'.$collMetadata['collectioncode'];
+					}
+					if($occArr['secondaryinstcode']){
+						$instCode .= ' || '.$occArr['secondaryinstcode'];
+						if(isset($occArr['secondarycollcode']) && $occArr['secondarycollcode']){
+							$instCode .= ':'.$occArr['secondarycollcode'];
+						}
+					}
 					?>
-					<div style="float:left;padding:25px;">
-						<span style="font-size:18px;font-weight:bold;vertical-align:60%;">
-							<?php echo $collMetadata['collectionname'].(!$iconUrl?' ('.$instCode.')':''); ?>
-						</span>
+					<div style="padding:25px;font-size:18px;font-weight:bold;">
+						<div style="float:left;margin-right:5px">
+							<?php echo $collMetadata['collectionname']; ?>
+						</div>
+						<div style="float:left;">
+							<?php echo '('.$instCode.')'; ?>
+						</div>
 					</div>
 					<div style="clear:both;margin-left:60px;">
 						<div>
diff --git a/collections/misc/collprofiles.php b/collections/misc/collprofiles.php
index db46d9d37e..ef84e799f1 100644
--- a/collections/misc/collprofiles.php
+++ b/collections/misc/collprofiles.php
@@ -366,7 +366,7 @@ function toggleById(target){
 						$dataUrl = 'http://www.gbif.org/dataset/'.$datasetKey;
 						?>
 						<div style="margin-top:5px;">
-							<div><b>GBIF Dataset page:</b> <a href="<?php echo $dataUrl; ?>" target="_blank"><?php echo $dataUrl; ?></a></div>
+							<div><b><?php echo (isset($LANG['GBIF_DATASET'])?$LANG['GBIF_DATASET']:'GBIF Dataset page'); ?>:</b> <a href="<?php echo $dataUrl; ?>" target="_blank"><?php echo $dataUrl; ?></a></div>
 						</div>
 						<?php
 					}
@@ -378,7 +378,7 @@ function toggleById(target){
 						$dataUrl = 'https://www.idigbio.org/portal/recordsets/'.$idigbioKey;
 						?>
 						<div style="margin-top:5px;">
-							<div><b>iDigBio Dataset page:</b> <a href="<?php echo $dataUrl; ?>" target="_blank"><?php echo $dataUrl; ?></a></div>
+							<div><b><?php echo (isset($LANG['IDIGBIO_DATASET'])?$LANG['IDIGBIO_DATASET']:'iDigBio Dataset page'); ?>:</b> <a href="<?php echo $dataUrl; ?>" target="_blank"><?php echo $dataUrl; ?></a></div>
 						</div>
 						<?php
 					}
@@ -386,11 +386,11 @@ function toggleById(target){
 				if($addrArr = $collManager->getAddress()){
 					?>
 					<div style="margin-top:5px;">
-						<div style="float:left;font-weight:bold;">Address:</div>
+						<div style="float:left;font-weight:bold;"><?php echo (isset($LANG['ADDRESS'])?$LANG['ADDRESS']:'Address'); ?>:</div>
 						<div style="float:left;margin-left:10px;">
 							<?php
 							echo "<div>".$addrArr["institutionname"];
-							if($editCode > 1) echo ' <a href="../admin/institutioneditor.php?emode=1&targetcollid='.$collid.'&iid='.$addrArr['iid'].'" title="Edit institution information"><img src="../../images/edit.png" style="width:13px;" /></a>';
+							if($editCode > 1) echo ' <a href="../admin/institutioneditor.php?emode=1&targetcollid='.$collid.'&iid='.$addrArr['iid'].'" title="'.(isset($LANG['EDIT_INST'])?$LANG['EDIT_INST']:'Edit institution information').'"><img src="../../images/edit.png" style="width:13px;" /></a>';
 							echo '</div>';
 							if($addrArr["institutionname2"]) echo "<div>".$addrArr["institutionname2"]."</div>";
 							if($addrArr["address1"]) echo "<div>".$addrArr["address1"]."</div>";
@@ -430,22 +430,22 @@ function toggleById(target){
 					<div style="font-weight:bold;"><?php echo $LANG['COLL_STATISTICS']; ?></div>
 					<ul style="margin-top:5px;">
 						<li><?php echo number_format($statsArr["recordcnt"]).' '.$LANG['SPECIMEN_RECORDS'];?></li>
-						<li><?php echo ($statsArr['georefcnt']?number_format($statsArr['georefcnt']):0).($georefPerc?" (".($georefPerc>1?round($georefPerc):round($georefPerc,2))."%)":'');?> georeferenced</li>
+						<li><?php echo ($statsArr['georefcnt']?number_format($statsArr['georefcnt']):0).($georefPerc?" (".($georefPerc>1?round($georefPerc):round($georefPerc,2))."%)":'').' '.(isset($LANG['GEOREFERENCED'])?$LANG['GEOREFERENCED']:'georeferenced');?></li>
 						<?php
 						if($extrastatsArr){
-							if($extrastatsArr['imgcnt']) echo '<li>'.number_format($extrastatsArr['imgcnt']).($imgPerc?" (".($imgPerc>1?round($imgPerc):round($imgPerc,2))."%)":'').' with images</li>';
-							if($extrastatsArr['gencnt']) echo '<li>'.number_format($extrastatsArr['gencnt']).' GenBank references</li>';
-							if($extrastatsArr['boldcnt']) echo '<li>'.number_format($extrastatsArr['boldcnt']).' BOLD references</li>';
-							if($extrastatsArr['refcnt']) echo '<li>'.number_format($extrastatsArr['refcnt']).' publication references</li>';
-							if($extrastatsArr['SpecimensCountID']) echo '<li>'.number_format($extrastatsArr['SpecimensCountID']).($spidPerc?" (".($spidPerc>1?round($spidPerc):round($spidPerc,2))."%)":'').' identified to species</li>';
+							if($extrastatsArr['imgcnt']) echo '<li>'.number_format($extrastatsArr['imgcnt']).($imgPerc?" (".($imgPerc>1?round($imgPerc):round($imgPerc,2))."%)":'').' '.(isset($LANG['WITH_IMAGES'])?$LANG['WITH_IMAGES']:'with images').'</li>';
+							if($extrastatsArr['gencnt']) echo '<li>'.number_format($extrastatsArr['gencnt']).' '.(isset($LANG['GENBANK_REF'])?$LANG['GENBANK_REF']:'GenBank references').'</li>';
+							if($extrastatsArr['boldcnt']) echo '<li>'.number_format($extrastatsArr['boldcnt']).' '.(isset($LANG['BOLD_REF'])?$LANG['BOLD_REF']:'BOLD references').'</li>';
+							if($extrastatsArr['refcnt']) echo '<li>'.number_format($extrastatsArr['refcnt']).' '.(isset($LANG['PUB_REFS'])?$LANG['PUB_REFS']:'publication references').'</li>';
+							if($extrastatsArr['SpecimensCountID']) echo '<li>'.number_format($extrastatsArr['SpecimensCountID']).($spidPerc?" (".($spidPerc>1?round($spidPerc):round($spidPerc,2))."%)":'').' '.(isset($LANG['IDED_TO_SPECIES'])?$LANG['IDED_TO_SPECIES']:'identified to species').'</li>';
 						}
 						?>
 						<li><?php echo number_format($statsArr["familycnt"]).' '.$LANG['FAMILIES'];?></li>
 						<li><?php echo number_format($statsArr["genuscnt"]).' '.$LANG['GENERA'];?></li>
 						<li><?php echo number_format($statsArr["speciescnt"]).' '.$LANG['SPECIES'];?></li>
 						<?php
-						if($extrastatsArr&&$extrastatsArr['TotalTaxaCount']) echo '<li>'.number_format($extrastatsArr['TotalTaxaCount']).' total taxa (including subsp. and var.)</li>';
-						//if($extrastatsArr&&$extrastatsArr['TypeCount']) echo '<li>'.number_format($extrastatsArr['TypeCount']).' type specimens</li>';
+						if($extrastatsArr&&$extrastatsArr['TotalTaxaCount']) echo '<li>'.number_format($extrastatsArr['TotalTaxaCount']).' '.(isset($LANG['TOTAL_TAXA'])?$LANG['TOTAL_TAXA']:'total taxa (including subsp. and var.)').'</li>';
+						//if($extrastatsArr&&$extrastatsArr['TypeCount']) echo '<li>'.number_format($extrastatsArr['TypeCount']).' '.(isset($LANG['TYPE_SPECIMENS'])?$LANG['TYPE_SPECIMENS']:'type specimens').'</li>';
 						?>
 					</ul>
 				</div>
@@ -464,7 +464,7 @@ function toggleById(target){
 		}
 		else{
 			?>
-			<h2><?php echo $DEFAULT_TITLE; ?> Natural History Collections and Observation Projects</h2>
+			<h2><?php echo $DEFAULT_TITLE.' '.(isset($LANG['COLLECTION_PROJECTS'])?$LANG['COLLECTION_PROJECTS']:'Natural History Collections and Observation Projects'); ?></h2>
 			<div style='margin:10px;clear:both;'>
 				<?php
 				$serverDomain = "http://";
diff --git a/content/lang/collections/misc/collprofiles.en.php b/content/lang/collections/misc/collprofiles.en.php
index e14bb68245..6ad1e28c3e 100644
--- a/content/lang/collections/misc/collprofiles.en.php
+++ b/content/lang/collections/misc/collprofiles.en.php
@@ -49,22 +49,38 @@
 $LANG['UPDATE_STATS'] = 'Update Statistics';
 $LANG['COLLECTION_TYPE'] = 'Collection Type';
 $LANG['MANAGEMENT'] = 'Management';
+$LANG['LIVE_DATA'] = 'Live Data managed directly within data portal';
+$LANG['DATA_AGGREGATE'] = 'Data harvested from a data aggregator';
+$LANG['DATA_SNAPSHOT'] = 'Data snapshot of local collection database';
 $LANG['LAST_UPDATE'] = 'Last Update';
 $LANG['GLOBAL_UNIQUE_ID'] = 'Global Unique Identifier';
 $LANG['DWCA_PUB'] = 'DwC-Archive Access Point';
 $LANG['LIVE_DOWNLOAD'] = 'Live Data Download';
 $LANG['FULL_DATA'] = 'DwC-Archive File';
-$LANG['LOGIN_TO_ACCESS'] = 'Login for access';
 $LANG['IPT_SOURCE'] = 'IPT / DwC-A Source';
 $LANG['DIGITAL_METADATA'] = 'Digital Metadata';
 $LANG['USAGE_RIGHTS'] = 'Usage Rights';
+$LANG['USAGE_POLICY'] = 'Usage policy';
 $LANG['RIGHTS_HOLDER'] = 'Rights Holder';
 $LANG['ACCESS_RIGHTS'] = 'Access Rights';
+
+$LANG['GBIF_DATASET'] = 'GBIF Dataset page';
+$LANG['IDIGBIO_DATASET'] = 'iDigBio Dataset page';
+$LANG['ADDRESS'] = 'Address';
+$LANG['EDIT_INST'] = 'Edit institution information';
 $LANG['COLL_STATISTICS'] = 'Collection Statistics';
 $LANG['SPECIMEN_RECORDS'] = 'specimen records';
+$LANG['GEOREFERENCED'] = 'georeferenced';
+$LANG['WITH_IMAGES'] = 'with images';
+$LANG['GENBANK_REF'] = 'GenBank references';
+$LANG['BOLD_REF'] = 'BOLD references';
+$LANG['PUB_REFS'] = 'publication references';
+$LANG['IDED_TO_SPECIES'] = 'identified to species';
 $LANG['FAMILIES'] = 'families';
 $LANG['GENERA'] = 'genera';
 $LANG['SPECIES'] = 'species';
+$LANG['TOTAL_TAXA'] = 'total taxa (including subsp. and var.)';
+$LANG['TYPE_SPECIMENS'] = 'type specimens';
 $LANG['EXTRA_STATS'] = 'Extra Statistics';
 $LANG['SHOW_FAMILY_DIST'] = 'Show Family Distribution';
 $LANG['HIDE_FAMILY_DIST'] = 'Hide Family Distribution';
@@ -75,4 +91,5 @@
 $LANG['TAXON_DIST'] = 'Taxon Distribution';
 $LANG['CLICK_ON_SPEC_FAM'] = 'Click on the specimen record counts within the parenthesis to return the records for that family';
 $LANG['GEOG_DIST_COUNTRIES'] = 'Geographic Distribution - Countries';
+$LANG['COLLECTION_PROJECTS'] = 'Natural History Collections and Observation Projects';
 ?>
\ No newline at end of file
diff --git a/content/lang/collections/misc/collprofiles.es.php b/content/lang/collections/misc/collprofiles.es.php
index dc5bf44b5f..644a487e30 100644
--- a/content/lang/collections/misc/collprofiles.es.php
+++ b/content/lang/collections/misc/collprofiles.es.php
@@ -49,22 +49,38 @@
 $LANG['UPDATE_STATS'] = 'Actualizar Estad&iacute;sticas';
 $LANG['COLLECTION_TYPE'] = 'Tipo de Colecci&oacute;n';
 $LANG['MANAGEMENT'] = 'Administraci&oacute;n';
+$LANG['LIVE_DATA'] = 'Datos en vivo administrados directamente dentro del portal de datos';
+$LANG['DATA_AGGREGATE'] = 'Datos recolectados de un agregador de datos';
+$LANG['DATA_SNAPSHOT'] = 'Instant&aacute;nea de datos de un base de datos local';
 $LANG['LAST_UPDATE'] = '&uacute;ltima Actualizaci&oacute;n';
 $LANG['GLOBAL_UNIQUE_ID'] = 'Identificador &uacute;nico Global';
 $LANG['DWCA_PUB'] = 'DwC-Archive Access Punto de Acceso';
 $LANG['LIVE_DOWNLOAD'] = 'Descarga de Datos en Vivo';
 $LANG['FULL_DATA'] = 'Archivo DwC-Archive';
-$LANG['LOGIN_TO_ACCESS'] = 'Iniciar Sesi&oacute;n para Acceder';
 $LANG['IPT_SOURCE'] = 'IPT / DwC-A';
 $LANG['DIGITAL_METADATA'] = 'Metadata Digital';
 $LANG['USAGE_RIGHTS'] = 'Derechos de Uso';
+$LANG['USAGE_POLICY'] = 'Pol&iacute;tica de uso';
 $LANG['RIGHTS_HOLDER'] = 'Propietario de Derechos';
 $LANG['ACCESS_RIGHTS'] = 'Derechos de Acceso';
+
+$LANG['GBIF_DATASET'] = 'Dato de GBIF';
+$LANG['IDIGBIO_DATASET'] = 'Datos de iDigBio';
+$LANG['ADDRESS'] = 'Direcci&oacute;n';
+$LANG['EDIT_INST'] = 'Revisar la informaci&oacute;n de la instituci&oacute;n';
 $LANG['COLL_STATISTICS'] = 'Estad&iacute;sticas de Colecci&oacute;n';
 $LANG['SPECIMEN_RECORDS'] = 'registros de espec&iacute;menes';
+$LANG['GEOREFERENCED'] = 'georeferenciado';
+$LANG['WITH_IMAGES'] = 'con imagenes';
+$LANG['GENBANK_REF'] = 'Referencias de GenBank';
+$LANG['BOLD_REF'] = 'Referencias de BOLD';
+$LANG['PUB_REFS'] = 'referencias de publicaciones';
+$LANG['IDED_TO_SPECIES'] = 'identificado a las especies';
 $LANG['FAMILIES'] = 'familias';
 $LANG['GENERA'] = 'g&eacute;neros';
 $LANG['SPECIES'] = 'especies';
+$LANG['TOTAL_TAXA'] = 'total taxa (including subsp. and var.)';
+$LANG['TYPE_SPECIMENS'] = 'type specimens';
 $LANG['EXTRA_STATS'] = 'Estad&iacute;sticas Extras';
 $LANG['SHOW_FAMILY_DIST'] = 'Mostrar Distribuci&oacute;n por Familia';
 $LANG['HIDE_FAMILY_DIST'] = 'Ocultar Distribuci&oacute;n por Familia';
@@ -75,4 +91,5 @@
 $LANG['TAXON_DIST'] = 'Distribuci&oacute;n de Taxon';
 $LANG['CLICK_ON_SPEC_FAM'] = 'Haga clic en los recuentos de registros de espec&iacute;menes dentro de los par&eacute;ntesis para mostrar los registros para esa familia';
 $LANG['GEOG_DIST_COUNTRIES'] = 'Distribuci&oacute;n Geogr&aacute;fica - Pa&iacute;ses';
+$LANG['COLLECTION_PROJECTS'] = 'Natural History Collections and Observation Projects';
 ?>
\ No newline at end of file
diff --git a/css/base.css b/css/base.css
index 43f950169c..995e009a40 100644
--- a/css/base.css
+++ b/css/base.css
@@ -252,6 +252,7 @@ div.button:hover {
 
 .collectiontitle{
 	font-size:12px;
+	margin-top:8px;
 }
 
 .collectiontitle a{

From 693313b31b812702eb95b01e6858e15f03c16cab Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Mon, 16 Sep 2019 21:06:48 -0700
Subject: [PATCH 11/23] Minor Collection Meta Display Adjustment

---
 classes/OccurrenceCollectionProfile.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/classes/OccurrenceCollectionProfile.php b/classes/OccurrenceCollectionProfile.php
index 1520760782..f7eb880f67 100644
--- a/classes/OccurrenceCollectionProfile.php
+++ b/classes/OccurrenceCollectionProfile.php
@@ -161,8 +161,8 @@ public function getMetadataHtml($collArr, $LANG){
 		}
 		$outStr .= '<div style="margin-top:5px;">';
 		if($collArr['managementtype'] == 'Live Data'){
-			$outStr .= '<b>'.(isset($LANG['LIVE_DOWNLOAD'])?$LANG['LIVE_DOWNLOAD']:'Live Data Download').':</b> ';
 			if($GLOBALS['SYMB_UID']){
+				$outStr .= '<b>'.(isset($LANG['LIVE_DOWNLOAD'])?$LANG['LIVE_DOWNLOAD']:'Live Data Download').':</b> ';
 				$outStr .= '<a href="../../webservices/dwc/dwcapubhandler.php?collid='.$collArr['collid'].'">'.(isset($LANG['FULL_DATA'])?$LANG['FULL_DATA']:'DwC-Archive File').'</a>';
 			}
 		}

From a3db9a7f9de11f3517a3dd5193b3f933a29ef790 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Fri, 20 Sep 2019 13:32:32 -0700
Subject: [PATCH 12/23] Misc layout adjustments and minor bug fixes

- Minor specimen upload bug
- Minor bug fix to UTM format tool
- Readjustment of public search form text
---
 classes/SpecUploadBase.php                    |  2 +-
 collections/harvestparams.php                 | 20 ++++++++++---------
 content/lang/collections/harvestparams.en.php |  4 +---
 content/lang/collections/harvestparams.es.php |  4 +---
 js/symb/collections.occureditortools.js       |  4 +++-
 5 files changed, 17 insertions(+), 17 deletions(-)

diff --git a/classes/SpecUploadBase.php b/classes/SpecUploadBase.php
index de360a7217..d3ae3c52dc 100644
--- a/classes/SpecUploadBase.php
+++ b/classes/SpecUploadBase.php
@@ -728,7 +728,7 @@ private function recordCleaningStage2(){
 			if($this->collMetadataArr["managementtype"] == 'Snapshot' || $this->uploadType == $this->SKELETAL){
 				//Match records that were processed via the portal, walked back to collection's central database, and come back to portal
 				$this->outputMsg('<li style="margin-left:10px;">Populating source identifiers (dbpk) to relink specimens processed within portal...</li>');
-				$sql = 'UPDATE uploadspectemp u INNER JOIN omoccurrences o ON (u.catalogNumber = o.catalogNumber) AND (u.collid = o.collid) '.
+				$sql = 'UPDATE IGNORE uploadspectemp u INNER JOIN omoccurrences o ON (u.catalogNumber = o.catalogNumber) AND (u.collid = o.collid) '.
 					'SET u.occid = o.occid, o.dbpk = u.dbpk '.
 					'WHERE (u.collid IN('.$this->collId.')) AND (u.occid IS NULL) AND (u.catalogNumber IS NOT NULL) AND (o.catalogNumber IS NOT NULL) AND (o.dbpk IS NULL) ';
 				$this->conn->query($sql);
diff --git a/collections/harvestparams.php b/collections/harvestparams.php
index d3f509d918..161e2ac363 100644
--- a/collections/harvestparams.php
+++ b/collections/harvestparams.php
@@ -32,6 +32,9 @@
 	<script type="text/javascript">
 		<?php include_once($SERVER_ROOT.'/config/googleanalytics.php'); ?>
 	</script>
+	<style type="text/css">
+		hr{ margin: 10px 0px }
+	</style>
 </head>
 <body>
 <?php
@@ -57,8 +60,6 @@
 	?>
 
 	<div id="innertext">
-		<h1><?php echo $LANG['PAGE_HEADER']; ?></h1>
-		<?php echo $LANG['GENERAL_TEXT_1']; ?>
 		<form name="harvestparams" id="harvestparams" action="list.php" method="post" onsubmit="return checkHarvestParamsForm(this)">
 			<div style="margin:10 0 10 0;"><hr/></div>
 			<div style='float:right;margin:-5px 10px;'>
@@ -67,10 +68,10 @@
 				<div><button type="reset" class="ui-button ui-widget ui-corner-all" style="padding:3px 10px;" onclick="resetHarvestParamsForm()"><?php echo isset($LANG['BUTTON_RESET'])?$LANG['BUTTON_RESET']:'Reset Form'; ?></button></div>
 			</div>
 			<div>
-				<h1><?php echo $LANG['TAXON_HEADER']; ?></h1>
+				<div style="font-weight:bold; font-size: 18px; margin-bottom: 10px;"><?php echo $LANG['TAXON_HEADER']; ?></div>
 				<span style="margin-left:5px;"><input type='checkbox' name='usethes' value='1' CHECKED /><?php echo $LANG['INCLUDE_SYNONYMS']; ?></span>
 			</div>
-			<div>
+			<div style="height: 45px">
 				<select id="taxontype" name="taxontype">
 					<?php
 					$taxonType = 1;
@@ -82,9 +83,9 @@
 				</select>
 				<input id="taxa" type="text" size="60" name="taxa" value="" title="<?php echo $LANG['SEPARATE_MULTIPLE']; ?>" />
 			</div>
-			<div style="margin:10 0 10 0;"><hr></div>
+			<hr/>
 			<div>
-				<h1><?php echo $LANG['LOCALITY_CRITERIA']; ?></h1>
+				<div style="font-weight:bold; font-size: 18px"><?php echo $LANG['LOCALITY_CRITERIA']; ?></div>
 			</div>
 			<div>
 				<?php echo $LANG['COUNTRY']; ?>: <input type="text" id="country" size="43" name="country" value="" title="<?php echo $LANG['SEPARATE_MULTIPLE']; ?>" />
@@ -104,7 +105,7 @@
 			</div>
 			<div style="margin:10 0 10 0;">
 				<hr>
-				<h1><?php echo $LANG['LAT_LNG_HEADER']; ?></h1>
+				<div style="font-weight:bold; font-size: 18px"><?php echo $LANG['LAT_LNG_HEADER']; ?></div>
 			</div>
 			<div style="float:left;border:2px solid brown;padding:10px;margin-bottom:10px;">
 				<div style="clear:both;float:right;">
@@ -184,7 +185,7 @@
 			</div>
 			<div style=";clear:both;"><hr/></div>
 			<div>
-				<h1><?php echo $LANG['COLLECTOR_HEADER']; ?></h1>
+				<div style="font-weight:bold; font-size: 18px"><?php echo $LANG['COLLECTOR_HEADER']; ?></div>
 			</div>
 			<div>
 				<?php echo $LANG['COLLECTOR_LASTNAME']; ?>:
@@ -199,12 +200,13 @@
 				<input type="text" id="eventdate1" size="32" name="eventdate1" style="width:100px;" value="" title="<?php echo $LANG['TITLE_TEXT_3']; ?>" /> -
 				<input type="text" id="eventdate2" size="32" name="eventdate2" style="width:100px;" value="" title="<?php echo $LANG['TITLE_TEXT_4']; ?>" />
 			</div>
+			<hr/>
 			<div style="float:right;">
 				<div><button type="submit" class="ui-button ui-widget ui-corner-all"><?php echo isset($LANG['BUTTON_NEXT_LIST'])?$LANG['BUTTON_NEXT_LIST']:'List Display'; ?></button></div>
 				<div style="margin-bottom:10px"><button type="button" class="ui-button ui-widget ui-corner-all" onclick="displayTableView(this.form)"><?php echo isset($LANG['BUTTON_NEXT_TABLE'])?$LANG['BUTTON_NEXT_TABLE']:'Table Display'; ?></button></div>
 			</div>
 			<div>
-				<h1><?php echo $LANG['SPECIMEN_HEADER']; ?></h1>
+				<div style="font-weight:bold; font-size: 18px"><?php echo $LANG['SPECIMEN_HEADER']; ?></div>
 			</div>
 			<div>
 				<?php echo $LANG['CATALOG_NUMBER']; ?>:
diff --git a/content/lang/collections/harvestparams.en.php b/content/lang/collections/harvestparams.en.php
index d187ad0428..e62e9861c1 100644
--- a/content/lang/collections/harvestparams.en.php
+++ b/content/lang/collections/harvestparams.en.php
@@ -8,9 +8,7 @@
 include_once('sharedterms.en.php');
 
 $LANG['PAGE_TITLE'] = 'Collection Search Parameters';
-$LANG['PAGE_HEADER'] = 'Enter Search Parameters';
-$LANG['GENERAL_TEXT_1'] = 'Fill in one or more of the following query criteria and click &quot;Search&quot; to view your results.';
-$LANG['TAXON_HEADER'] = 'Taxonomic Criteria:';
+$LANG['TAXON_HEADER'] = 'Taxonomic Criteria';
 $LANG['INCLUDE_SYNONYMS'] = 'Include Synonyms';
 $LANG['BUTTON_NEXT_LIST'] = 'List Display';
 $LANG['BUTTON_NEXT_TABLE'] = 'Table Display';
diff --git a/content/lang/collections/harvestparams.es.php b/content/lang/collections/harvestparams.es.php
index 24046abdd8..54fcc68c91 100644
--- a/content/lang/collections/harvestparams.es.php
+++ b/content/lang/collections/harvestparams.es.php
@@ -8,9 +8,7 @@
 include_once('sharedterms.es.php');
 
 $LANG['PAGE_TITLE'] = 'Par&aacute;metros de B&uacute;squeda de Colecciones';
-$LANG['PAGE_HEADER'] = 'Formulario de B&uacute;squeda';
-$LANG['GENERAL_TEXT_1'] = 'Ingrese uno o m&aacute;s de los criterios de consulta siguientes y haga click en el bot&oacute;n &quot;Search&quot; para ver los resultados.';
-$LANG['TAXON_HEADER'] = 'Criterios Taxonomicos:';
+$LANG['TAXON_HEADER'] = 'Criterios Taxonomicos';
 $LANG['INCLUDE_SYNONYMS'] = 'Incluir Sin&oacute;nimos';
 $LANG['BUTTON_NEXT_LIST'] = 'Mostrar Lista';
 $LANG['BUTTON_NEXT_TABLE'] = 'Mostrar Tabla';
diff --git a/js/symb/collections.occureditortools.js b/js/symb/collections.occureditortools.js
index 0ae63790b0..2293450c91 100644
--- a/js/symb/collections.occureditortools.js
+++ b/js/symb/collections.occureditortools.js
@@ -163,7 +163,9 @@ function insertUtm(f) {
 			if(vcStr != ""){
 				vcStr = vcStr + "; ";
 			}
-			var utmStr = zValue + hValue + " " + eValue + "E " + nValue + "N ";
+			var utmStr = zValue;
+			if(isNumeric(zValue)) utmStr = utmStr + hValue;
+			utmStr = utmStr + " " + eValue + "E " + nValue + "N ";
 			f.verbatimcoordinates.value = vcStr + utmStr;
 			//Convert to Lat/Lng values
 			var zNum = parseInt(zValue);

From 601d31f0eaedcbb9368e8cdcc3df88339c9f5d1a Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Fri, 20 Sep 2019 16:05:48 -0700
Subject: [PATCH 13/23] Paleo Development

- Add Bed field
- Change Storage Age to be free form field
- Reposition lithology field size and placement
- Setup basisOfField to denote FossilSpecimen for paleo collections
---
 classes/OccurrenceEditorManager.php          |  4 +-
 classes/OccurrenceIndividualManager.php      |  2 +-
 collections/editor/includes/paleoinclude.php | 16 +++----
 collections/editor/occurrenceeditor.php      | 47 +++++++++++---------
 collections/individual/index.php             | 32 ++++++-------
 css/occureditor.css                          |  2 +
 6 files changed, 52 insertions(+), 51 deletions(-)

diff --git a/classes/OccurrenceEditorManager.php b/classes/OccurrenceEditorManager.php
index 37944b91f3..ec28fe2cea 100644
--- a/classes/OccurrenceEditorManager.php
+++ b/classes/OccurrenceEditorManager.php
@@ -51,7 +51,7 @@ public function __construct($conn = null){
 			'labelproject','observeruid','basisofrecord','institutioncode','collectioncode','ownerinstitutioncode','datelastmodified', 'processingstatus',
 			'recordenteredby', 'dateentered');
 		$this->paleoFieldArr = array('eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','element','slideproperties');
+			'biostratigraphy','lithogroup','formation','taxonenvironment','member','bed','lithology','stratremarks','element','slideproperties');
 	}
 
 	public function __destruct(){
@@ -1634,7 +1634,7 @@ public function carryOverValues($fArr){
 			'minimumelevationinmeters','maximumelevationinmeters','verbatimelevation','minimumdepthinmeters','maximumdepthinmeters','verbatimdepth',
 			'habitat','substrate','lifestage', 'sex', 'individualcount', 'samplingprotocol', 'preparations',
 			'associatedtaxa','basisofrecord','language','labelproject','eon','era','period','epoch','earlyinterval','lateinterval','absoluteage','storageage','stage','localstage','biota',
-			'biostratigraphy','lithogroup','formation','taxonenvironment','member','lithology','stratremarks','element');
+			'biostratigraphy','lithogroup','formation','taxonenvironment','member','bed','lithology','stratremarks','element');
 		$retArr = $this->cleanOutArr(array_intersect_key($fArr,array_flip($locArr)));
 		return $retArr;
 	}
diff --git a/classes/OccurrenceIndividualManager.php b/classes/OccurrenceIndividualManager.php
index 430ddde545..da1b414efc 100644
--- a/classes/OccurrenceIndividualManager.php
+++ b/classes/OccurrenceIndividualManager.php
@@ -220,7 +220,7 @@ private function loadImages(){
 
 	private function loadPaleo(){
 		$sql = 'SELECT paleoid, eon, era, period, epoch, earlyinterval, lateinterval, absoluteage, storageage, stage, localstage, biota, '.
-			'biostratigraphy, lithogroup, formation, taxonenvironment, member, lithology, stratremarks, element, slideproperties '.
+			'biostratigraphy, lithogroup, formation, taxonenvironment, member, bed, lithology, stratremarks, element, slideproperties '.
 			'FROM omoccurpaleo WHERE occid = '.$this->occid;
 		$rs = $this->conn->query($sql);
 		if($rs){
diff --git a/collections/editor/includes/paleoinclude.php b/collections/editor/includes/paleoinclude.php
index 6ffbeb8faf..995316083e 100644
--- a/collections/editor/includes/paleoinclude.php
+++ b/collections/editor/includes/paleoinclude.php
@@ -193,14 +193,7 @@ function setPaloParents(timePeriod){
 		<div id="storageAgeDiv">
 			<?php echo (defined('STORAGEAGELABEL')?STORAGEAGELABEL:'Storage Age'); ?>
 			<a href="#" onclick="return dwcDoc('storageAge')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
-			<select name="storageage" onchange="fieldChanged('storageage');">
-				<option value=""></option>
-				<?php
-				foreach($gtsTermArr as $term => $rankid){
-					if($rankid == 60) echo '<option value="'.$term.'" '.(isset($occArr['storageage']) && $occArr['storageage']==$term?'SELECTED':'').'>'.$term.'</option>';
-				}
-				?>
-			</select>
+			<input type="text" name="storageage" value="<?php echo isset($occArr['storageage'])?$occArr['storageage']:''; ?>" onchange="fieldChanged('storageage');" />
 		</div>
 		<div id="localStageDiv">
 			<?php echo (defined('LOCALSTAGELABEL')?LOCALSTAGELABEL:'Local Stage'); ?>
@@ -250,6 +243,13 @@ function setPaloParents(timePeriod){
 			<a href="#" onclick="return dwcDoc('member')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 			<input type="text" name="member" value="<?php echo isset($occArr['member'])?$occArr['member']:''; ?>" onchange="fieldChanged('member');" />
 		</div>
+		<div id="bedDiv">
+			<?php echo (defined('BEDLABEL')?BEDLABEL:'Bed'); ?>
+			<a href="#" onclick="return dwcDoc('bed')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
+			<input type="text" name="bed" value="<?php echo isset($occArr['bed'])?$occArr['bed']:''; ?>" onchange="fieldChanged('bed');" />
+		</div>
+	</div>
+	<div style="clear:both">
 		<div id="lithologyDiv">
 			<?php echo (defined('LITHOLOGYLABEL')?LITHOLOGYLABEL:'Lithology'); ?>
 			<a href="#" onclick="return dwcDoc('lithology')" tabindex="-1"><img class="docimg" src="../../images/qmark.png" /></a><br/>
diff --git a/collections/editor/occurrenceeditor.php b/collections/editor/occurrenceeditor.php
index 3f296080ea..5e645a17bb 100644
--- a/collections/editor/occurrenceeditor.php
+++ b/collections/editor/occurrenceeditor.php
@@ -36,6 +36,7 @@
 $displayQuery = 0;
 $isGenObs = 0;
 $collMap = Array();
+$collType = 'spec';
 $occArr = array();
 $imgArr = array();
 $specImgArr = array();
@@ -54,8 +55,19 @@
 		$collId = $collMap['collid'];
 		$occManager->setCollId($collId);
 	}
-	$editorPropArr = $occManager->getDynamicPropertiesArr();
-	if($collMap && $collMap['colltype']=='General Observations') $isGenObs = 1;
+	if($collMap){
+		$editorPropArr = $occManager->getDynamicPropertiesArr();
+		if($collMap['colltype']=='General Observations'){
+			$isGenObs = 1;
+			$collType = 'obs';
+		}
+		elseif($collMap['colltype']=='Observations'){
+			$collType = 'obs';
+		}
+		elseif(isset($editorPropArr['modules-panel']['paleo']['status']) && $editorPropArr['modules-panel']['paleo']['status']){
+			$collType = 'paleo';
+		}
+	}
 
 	//Bring in config variables
 	if($isGenObs){
@@ -465,7 +477,7 @@ function requestImage(){
 	<script src="../../js/symb/collections.coordinateValidation.js?ver=170310" type="text/javascript"></script>
 	<script src="../../js/symb/wktpolygontools.js?ver=180208" type="text/javascript"></script>
 	<script src="../../js/symb/collections.occureditormain.js?ver=201904" type="text/javascript"></script>
-	<script src="../../js/symb/collections.occureditortools.js?ver=1906" type="text/javascript"></script>
+	<script src="../../js/symb/collections.occureditortools.js?ver=1909" type="text/javascript"></script>
 	<script src="../../js/symb/collections.occureditorimgtools.js?ver=170310" type="text/javascript"></script>
 	<script src="../../js/jquery.imagetool-1.7.js?ver=140310" type="text/javascript"></script>
 	<script src="../../js/symb/collections.occureditorshare.js?ver=20180711" type="text/javascript"></script>
@@ -1133,7 +1145,7 @@ function requestImage(){
 											</div>
 										</fieldset>
 										<?php
-										if(isset($editorPropArr['modules-panel']['paleo']['status']) && $editorPropArr['modules-panel']['paleo']['status']) include('includes/paleoinclude.php');
+										if($collType == 'paleo') include('includes/paleoinclude.php');
 										?>
 										<fieldset>
 											<legend><b>Misc</b></legend>
@@ -1283,32 +1295,23 @@ function requestImage(){
 													<?php echo (defined('BASISOFRECORDLABEL')?BASISOFRECORDLABEL:'Basis of Record'); ?>
 													<a href="#" onclick="return dwcDoc('basisOfRecord')"><img class="docimg" src="../../images/qmark.png" /></a><br/>
 													<?php
-													$borArr = array('FossilSpecimen','HumanObservation','LivingSpecimen','MachineObservation','PreservedSpecimen');
-													$targetBOR = '';
-													$extraBOR = '';
+													$borArr = array('FossilSpecimen'=>0,'HumanObservation'=>0,'LivingSpecimen'=>0,'MachineObservation'=>0,'PreservedSpecimen'=>0);
 													if(isset($occArr['basisofrecord']) && $occArr['basisofrecord']){
-														if(in_array($occArr['basisofrecord'],$borArr)){
-															$targetBOR = $occArr['basisofrecord'];
-														}
-														else{
-															$extraBOR = $occArr['basisofrecord'];
-														}
+														if(in_array($occArr['basisofrecord'],$borArr)) $borArr[$occArr['basisofrecord']] = 1;
+														else $borArr[$occArr['basisofrecord']] = 2;
 													}
 													if(!isset($occArr['basisofrecord']) || !$occArr['basisofrecord']){
-														if($collMap['colltype']=='General Observations' || $collMap['colltype']=='Observations'){
-															$targetBOR = 'HumanObservation';
-														}
-														elseif($collMap['colltype']=='Preserved Specimens'){
-															$targetBOR = 'PreservedSpecimen';
-														}
+														if($collType == 'obs') $borArr['HumanObservation'] = 1;
+														elseif($collType == 'paleo') $borArr['FossilSpecimen'] = 1;
+														elseif($collType == 'spec') $borArr['PreservedSpecimen'] = 1;
 													}
 													?>
 													<select name="basisofrecord" tabindex="109" onchange="fieldChanged('basisofrecord');">
 														<?php
-														foreach($borArr as $bValue){
-															echo '<option '.($bValue == $targetBOR?'SELECTED':'').'>'.$bValue.'</option>';
+														foreach($borArr as $bValue => $statueCode){
+															if($statueCode == 2) echo '<option value="">---Non Sanctioned Value---</option><option SELECTED>'.$bValue.'</option>';
+															else echo '<option '.($statueCode?'SELECTED':'').'>'.$bValue.'</option>';
 														}
-														if($extraBOR) echo '<option value="">---Non Sanctioned Value---</option><option SELECTED>'.$extraBOR.'</option>';
 														?>
 													</select>
 												</div>
diff --git a/collections/individual/index.php b/collections/individual/index.php
index 1f8eaa69a7..e51bac43ee 100644
--- a/collections/individual/index.php
+++ b/collections/individual/index.php
@@ -775,24 +775,20 @@ function initializeMap(){
 								<div style="margin-left:10px">
 									<?php
 									$paleoStr2 = '';
-									if($occArr['absoluteage']) $paleoStr2 .= '; <b>absolute age:</b> '.$occArr['absoluteage'];
-									if($occArr['storageage']) $paleoStr2 .= '; <b>storage age:</b> '.$occArr['storageage'];
-									if($occArr['localstage']) $paleoStr2 .= '; <b>local stage:</b> '.$occArr['localstage'];
-									if($occArr['biota']) $paleoStr2 .= '; <b>biota:</b> '.$occArr['biota'];
-									if($occArr['biostratigraphy']) $paleoStr2 .= '; <b>biostratigraphy:</b> '.$occArr['biostratigraphy'];
-									if($paleoStr2) echo '<div>'.trim($paleoStr2,'; ').'<div>';
-									$paleoStr3 = '';
-									if($occArr['lithogroup']) $paleoStr3 .= '; <b>group:</b> '.$occArr['lithogroup'];
-									if($occArr['formation']) $paleoStr3 .= '; <b>formation:</b> '.$occArr['formation'];
-									if($occArr['taxonenvironment']) $paleoStr3 .= '; <b>taxon environment:</b> '.$occArr['taxonenvironment'];
-									if($occArr['member']) $paleoStr3 .= '; <b>member:</b> '.$occArr['member'];
-									if($occArr['lithology']) $paleoStr3 .= '; <b>lithology:</b> '.$occArr['lithology'];
-									if($paleoStr3) echo '<div>'.trim($paleoStr3,'; ').'</div>';
-									if($occArr['stratremarks']) echo '<div><b>remarks:</b> '.$occArr['stratremarks'].'</div>';
-									$paleoStr4 = '';
-									if($occArr['element']) $paleoStr4 .= '; <b>element:</b> '.$occArr['element'];
-									if($occArr['slideproperties']) $paleoStr4 .= '; <b>slide properties:</b> '.$occArr['slideproperties'];
-									if($paleoStr4) echo '<div>'.trim($paleoStr4,'; ').'</div>';
+									if($occArr['absoluteage']) echo '<div style="float:left;margin-right:25px"><b>absolute age:</b> '.$occArr['absoluteage'].'</div>';
+									if($occArr['storageage']) echo '<div style="float:left;margin-right:25px"><b>storage age:</b> '.$occArr['storageage'].'</div>';
+									if($occArr['localstage']) echo '<div style="float:left;margin-right:25px"><b>local stage:</b> '.$occArr['localstage'].'</div>';
+									if($occArr['biota']) echo '<div style="float:left;margin-right:25px"><b>biota:</b> '.$occArr['biota'].'</div>';
+									if($occArr['biostratigraphy']) echo '<div style="float:left;margin-right:25px"><b>biostratigraphy:</b> '.$occArr['biostratigraphy'].'</div>';
+									if($occArr['lithogroup']) echo '<div style="float:left;margin-right:25px"><b>group:</b> '.$occArr['lithogroup'].'</div>';
+									if($occArr['formation']) echo '<div style="float:left;margin-right:25px"><b>formation:</b> '.$occArr['formation'].'</div>';
+									if($occArr['taxonenvironment']) echo '<div style="float:left;margin-right:25px"><b>taxon environment:</b> '.$occArr['taxonenvironment'].'</div>';
+									if($occArr['member']) echo '<div style="float:left;margin-right:25px"><b>member:</b> '.$occArr['member'].'</div>';
+									if($occArr['bed']) echo '<div style="float:left;margin-right:25px"><b>bed:</b> '.$occArr['bed'].'</div>';
+									if($occArr['lithology']) echo '<div style="float:left;margin-right:25px"><b>lithology:</b> '.$occArr['lithology'].'</div>';
+									if($occArr['stratremarks']) echo '<div style="float:left;margin-right:25px"><b>remarks:</b> '.$occArr['stratremarks'].'</div>';
+									if($occArr['element']) echo '<div style="float:left;margin-right:25px"><b>element:</b> '.$occArr['element'].'</div>';
+									if($occArr['slideproperties']) echo '<div style="float:left;margin-right:25px"><b>slide properties:</b> '.$occArr['slideproperties'].'</div>';
 									?>
 								</div>
 							</div>
diff --git a/css/occureditor.css b/css/occureditor.css
index 42e18f7cd4..a1e3bde1ca 100644
--- a/css/occureditor.css
+++ b/css/occureditor.css
@@ -817,7 +817,9 @@ body{
 #formationDiv{ float:left; margin:3px; }
 #taxonEnvironmentDiv{ float:left; margin:3px; }
 #memberDiv{ float:left; margin:3px; }
+#bedDiv{ float:left; margin:3px; }
 #lithologyDiv{ float:left; margin:3px; }
+#lithologyDiv input{ width:600px; }
 #stratRemarksDiv{ float:left; margin:3px; }
 #stratRemarksDiv input{ width:600px; }
 #elementDiv{ float:left; margin:3px; }

From b835ed494209619b33e4743284546ba1988d24a2 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Fri, 20 Sep 2019 17:41:32 -0700
Subject: [PATCH 14/23] Occurrence Trait Development

---
 classes/OccurrenceAttributes.php              | 61 +++++++++++--------
 collections/traitattr/attributemining.php     |  6 +-
 .../dev/db_schema_patch_pending.sql           | 31 +++++++++-
 js/symb/collections.traitattr.js              |  4 +-
 4 files changed, 71 insertions(+), 31 deletions(-)

diff --git a/classes/OccurrenceAttributes.php b/classes/OccurrenceAttributes.php
index c207eec54f..017bbee236 100644
--- a/classes/OccurrenceAttributes.php
+++ b/classes/OccurrenceAttributes.php
@@ -27,7 +27,7 @@ public function addAttributes($postArr,$uid){
 		$status = true;
 		$stateArr = array();
 		foreach($postArr as $postKey => $postValue){
-			if(substr($postKey,0,8) == 'stateid-'){
+			if(substr($postKey,0,8) == 'traitid-'){
 				if(is_array($postValue)){
 					$stateArr = array_merge($stateArr,$postValue);
 				}
@@ -36,23 +36,35 @@ public function addAttributes($postArr,$uid){
 				}
 			}
 		}
-		$sourceStr = 'viewingSpecimenImage';
-		if(isset($postArr['source']) && $postArr['source']) $sourceStr = $postArr['source'];
-		foreach($stateArr as $stateId){
-			if(is_numeric($stateId)){
-				$sql = 'INSERT INTO tmattributes(stateid,occid,source,notes,createduid) '.
-					'VALUES('.$stateId.','.$this->occid.','.($sourceStr?'"'.$this->cleanInStr($sourceStr).'"':'NULL').','.
-					($postArr['notes']?'"'.$this->cleanInStr($postArr['notes']).'"':'NULL').','.$uid.') ';
-				//echo $sql.'<br/>';
-				if(!$this->conn->query($sql)){
-					$this->errorMessage .= 'ERROR saving occurrence attribute: '.$this->conn->error.'; ';
+		if($stateArr){
+			//Get trait types
+			$traitArr = array();
+			$sql = 'SELECT s.stateid, t.traittype FROM tmtraits t INNER JOIN tmstates s ON t.traitid = s.traitid WHERE s.stateid IN('.implode(',',$stateArr).')';
+			$rs = $this->conn->query($sql);
+			while($r = $rs->fetch_object()){
+				$traitArr[$r->stateid] = $r->traittype;
+			}
+			$rs->free();
+
+			//Insert attributes
+			$sourceStr = 'viewingSpecimenImage';
+			if(isset($postArr['source']) && $postArr['source']) $sourceStr = $postArr['source'];
+			foreach($stateArr as $stateId){
+				if(is_numeric($stateId)){
+					$sql = 'INSERT INTO tmattributes(stateid,xvalue,occid,source,notes,createduid) '.
+						'VALUES('.$stateId.',,'.$this->occid.','.($sourceStr?'"'.$this->cleanInStr($sourceStr).'"':'NULL').','.
+						($postArr['notes']?'"'.$this->cleanInStr($postArr['notes']).'"':'NULL').','.$uid.') ';
+					//echo $sql.'<br/>';
+					if(!$this->conn->query($sql)){
+						$this->errorMessage .= 'ERROR saving occurrence attribute: '.$this->conn->error.'; ';
+						$status = false;
+					}
+				}
+				else{
+					$this->errorMessage .= 'ERROR saving occurrence attribute: bad input values ('.$stateId.'); ';
 					$status = false;
 				}
 			}
-			else{
-				$this->errorMessage .= 'ERROR saving occurrence attribute: bad input values ('.$stateId.'); ';
-				$status = false;
-			}
 		}
 		return $status;
 	}
@@ -62,7 +74,7 @@ public function editAttributes($postArr){
 		$stateArr = array();
 
 		foreach($postArr as $postKey => $postValue){
-			if(substr($postKey,0,8) == 'stateid-'){
+			if(substr($postKey,0,8) == 'traitid-'){
 				if(is_array($postValue)){
 					$stateArr = array_merge($stateArr,$postValue);
 				}
@@ -89,7 +101,7 @@ public function editAttributes($postArr){
 							$status = true;
 						}
 						else{
-							$this->errorMessage = 'ERROR addin occurrence attribute: '.$this->conn->error;
+							$this->errorMessage = 'ERROR adding occurrence attribute: '.$this->conn->error;
 							$status = false;
 						}
 					}
@@ -253,8 +265,8 @@ public function getTraitArr($traitID = null, $setAttributes = true){
 	}
 
 	private function setTraitArr($traitID){
-		$sql = 'SELECT traitid, traitname, traittype, units, description, refurl, notes, dynamicproperties FROM tmtraits ';
-		if($traitID) $sql .= 'WHERE (traitid = '.$traitID.')';
+		$sql = 'SELECT traitid, traitname, traittype, units, description, refurl, notes, dynamicproperties FROM tmtraits WHERE traittype IN("UM","OM","NU") ';
+		if($traitID) $sql .= 'AND (traitid = '.$traitID.')';
 		//echo $sql.'<br/>';
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
@@ -305,14 +317,14 @@ private function setTraitStates(){
 
 	private function setCodedAttribute(){
 		$retArr = array();
-		$sql = 'SELECT s.traitid, a.stateid, a.source, a.notes, a.statuscode, a.modifieduid, a.datelastmodified, a.createduid, a.initialtimestamp '.
+		$sql = 'SELECT s.traitid, a.stateid, a.xvalue, a.source, a.notes, a.statuscode, a.modifieduid, a.datelastmodified, a.createduid, a.initialtimestamp '.
 			'FROM tmattributes a INNER JOIN tmstates s ON a.stateid = s.stateid '.
 			'WHERE (a.occid = '.$this->occid.') ';
 		if($this->traitArr) $sql .= 'AND (s.traitid IN('.implode(',',array_keys($this->traitArr)).'))';
 		//echo $sql; exit;
 		$rs = $this->conn->query($sql);
 		while($r = $rs->fetch_object()){
-			$this->traitArr[$r->traitid]['states'][$r->stateid]['coded'] = '';
+			$this->traitArr[$r->traitid]['states'][$r->stateid]['coded'] = $r->xvalue;
 			$this->traitArr[$r->traitid]['states'][$r->stateid]['source'] = $r->source;
 			$this->traitArr[$r->traitid]['states'][$r->stateid]['notes'] = $r->notes;
 			$this->traitArr[$r->traitid]['states'][$r->stateid]['statuscode'] = $r->statuscode;
@@ -342,19 +354,20 @@ private function getTraitUnitString($traitID,$display,$classStr=''){
 			foreach($attrStateArr as $sid => $sArr){
 				$isCoded = false;
 				if(array_key_exists('coded',$sArr)){
-					$isCoded = true;
+					if($sArr['coded'] === '') $isCoded = true;
+					else $isCoded = $sArr['coded'];
 					$this->stateCodedArr[$sid] = $sid;
 				}
 				$depTraitId = false;
 				if(isset($sArr['dependTraitID']) && $sArr['dependTraitID']) $depTraitId = $sArr['dependTraitID'];
 				if($controlType == 'checkbox' || $controlType == 'radio'){
-					$innerStr .= '<div title="'.$sArr['description'].'"><input name="stateid-'.$traitID.'[]" class="'.$classStr.'" type="'.$controlType.'" value="'.$sid.'" '.($isCoded?'checked':'').' onchange="traitChanged(this)" /> '.$sArr['name'];
+					$innerStr .= '<div title="'.$sArr['description'].'"><input name="traitid-'.$traitID.'[]" class="'.$classStr.'" type="'.$controlType.'" value="'.$sid.'" '.($isCoded?'checked':'').' onchange="traitChanged(this)" /> '.$sArr['name'];
 				}
 				elseif($controlType == 'select'){
 					$innerStr .= '<option value="'.$sid.'" '.($isCoded?'selected':'').'>'.$sArr['name'].'</option>';
 				}
 				elseif($controlType == 'numeric'){
-					$innerStr .= '<div title="'.$sArr['description'].'">'.$sArr['name'].': <input name="stateid-'.$traitID.'[]" class="'.$classStr.'" type="input" value="'.$sid.'" onchange="traitChanged(this)" style="width:50px" /> ';
+					$innerStr .= '<div title="'.$sArr['description'].'">'.$sArr['name'].': <input name="traitid-'.$traitID.'[]" class="'.$classStr.'" type="input" value="'.($isCoded!==false?$isCoded:'').'" onchange="traitChanged(this)" style="width:50px" /> ';
 				}
 				if($depTraitId){
 					$innerStr .= $this->getTraitUnitString($depTraitId,$isCoded,trim($classStr.' child-'.$sid));
diff --git a/collections/traitattr/attributemining.php b/collections/traitattr/attributemining.php
index 513a433142..ffa0fe4afc 100644
--- a/collections/traitattr/attributemining.php
+++ b/collections/traitattr/attributemining.php
@@ -58,7 +58,7 @@
 			if(!is_array($fieldValueArr)) $fieldValueArr = array($fieldValueArr);
 			$stateIDArr = array();
 			foreach($_POST as $postKey => $postValue){
-				if(substr($postKey,0,8) == 'stateid-'){
+				if(substr($postKey,0,8) == 'traitid-'){
 					if(is_array($postValue)){
 						$stateIDArr = array_merge($stateIDArr,$postValue);
 					}
@@ -110,7 +110,7 @@ function verifyMiningForm(f){
 				}
 
 				var formVerified = false;
-				$('input[name^="stateid-"]').each(function(){
+				$('input[name^="traitid-"]').each(function(){
 					if(this.checked == true){
 						formVerified = true;
 						return false;
@@ -160,7 +160,7 @@ function displayDetailDiv(spanObj){
 		<script src="../../js/symb/collections.traitattr.js" type="text/javascript"></script>
 		<script src="../../js/symb/shared.js" type="text/javascript"></script>
 	</head>
-	<body style="width:900px">
+	<body>
 		<?php
 		$displayLeftMenu = false;
 		include($SERVER_ROOT.'/header.php');
diff --git a/config/schema-1.0/dev/db_schema_patch_pending.sql b/config/schema-1.0/dev/db_schema_patch_pending.sql
index 23fef85d7e..9c2cae004b 100644
--- a/config/schema-1.0/dev/db_schema_patch_pending.sql
+++ b/config/schema-1.0/dev/db_schema_patch_pending.sql
@@ -9,6 +9,27 @@ ALTER TABLE `fmprojects`
 ALTER TABLE `fmchklstprojlink` 
    ADD COLUMN `sortSequence` INT NULL AFTER `mapChecklist`;
 
+
+ALTER TABLE `uploadspectemp` 
+  ADD COLUMN `geologicalcontextid` VARCHAR(150) NULL AFTER `exsiccatiNotes`,
+  ADD COLUMN `earliestEonOrLowestEonothem` VARCHAR(255) NULL AFTER `geologicalcontextid`,
+  ADD COLUMN `latestEonOrHighestEonothem` VARCHAR(255) NULL AFTER `earliestEonOrLowestEonothem`,
+  ADD COLUMN `earliestEraOrLowestErathem` VARCHAR(255) NULL AFTER `latestEonOrHighestEonothem`,
+  ADD COLUMN `latestEraOrHighestErathem` VARCHAR(255) NULL AFTER `earliestEraOrLowestErathem`,
+  ADD COLUMN `earliestPeriodOrLowestSystem` VARCHAR(255) NULL AFTER `latestEraOrHighestErathem`,
+  ADD COLUMN `latestPeriodOrHighestSystem` VARCHAR(255) NULL AFTER `earliestPeriodOrLowestSystem`,
+  ADD COLUMN `earliestEpochOrLowestSeries` VARCHAR(255) NULL AFTER `latestPeriodOrHighestSystem`,
+  ADD COLUMN `latestEpochOrHighestSeries` VARCHAR(255) NULL AFTER `earliestEpochOrLowestSeries`,
+  ADD COLUMN `earliestAgeOrLowestStage` VARCHAR(255) NULL AFTER `latestEpochOrHighestSeries`,
+  ADD COLUMN `latestAgeOrHighestStage` VARCHAR(255) NULL AFTER `earliestAgeOrLowestStage`,
+  ADD COLUMN `lowestBiostratigraphicZone` VARCHAR(255) NULL AFTER `latestAgeOrHighestStage`,
+  ADD COLUMN `highestBiostratigraphicZone` VARCHAR(255) NULL AFTER `lowestBiostratigraphicZone`,
+  ADD COLUMN `lithostratigraphicTermsProperty` VARCHAR(255) NULL AFTER `highestBiostratigraphicZone`,
+  ADD COLUMN `group` VARCHAR(255) NULL AFTER `lithostratigraphicTermsProperty`,
+  ADD COLUMN `formation` VARCHAR(255) NULL AFTER `group`,
+  ADD COLUMN `member` VARCHAR(255) NULL AFTER `formation`,
+  ADD COLUMN `bed` VARCHAR(255) NULL AFTER `member`;
+
 ALTER TABLE `uploadspectemp` 
   CHANGE COLUMN `basisOfRecord` `basisOfRecord` VARCHAR(32) NULL DEFAULT NULL COMMENT 'PreservedSpecimen, LivingSpecimen, HumanObservation' ;
 
@@ -76,11 +97,12 @@ CREATE TABLE `omoccurpaleo` (
   `localStage` VARCHAR(65) NULL,
   `biota` VARCHAR(65) NULL COMMENT 'Flora or Fanua',
   `biostratigraphy` VARCHAR(65) NULL COMMENT 'Biozone',
+  `taxonEnvironment` VARCHAR(65) NULL COMMENT 'Marine or not',
   `lithogroup` VARCHAR(65) NULL,
   `formation` VARCHAR(65) NULL,
-  `taxonEnvironment` VARCHAR(65) NULL COMMENT 'Marine or not',
   `member` VARCHAR(65) NULL,
-  `lithology` VARCHAR(65) NULL,
+  `bed` VARCHAR(65) NULL,
+  `lithology` VARCHAR(250) NULL,
   `stratRemarks` VARCHAR(250) NULL,
   `element` VARCHAR(250) NULL,
   `slideProperties` VARCHAR(1000) NULL,
@@ -91,6 +113,11 @@ CREATE TABLE `omoccurpaleo` (
   CONSTRAINT `FK_paleo_occid`  FOREIGN KEY (`occid`)  REFERENCES `omoccurrences` (`occid`)  ON DELETE CASCADE  ON UPDATE CASCADE
 ) COMMENT = 'Occurrence Paleo tables';
 
+#ALTER TABLE `omoccurpaleo` 
+#CHANGE COLUMN `taxonEnvironment` `taxonEnvironment` VARCHAR(65) NULL DEFAULT NULL COMMENT 'Marine or not' AFTER `biostratigraphy`,
+#CHANGE COLUMN `lithology` `lithology` VARCHAR(250) NULL DEFAULT NULL ,
+#ADD COLUMN `bed` VARCHAR(65) NULL AFTER `member`;
+
 CREATE TABLE `omoccurpaleogts` (
   `gtsid` INT UNSIGNED NOT NULL AUTO_INCREMENT,
   `gtsterm` VARCHAR(45) NOT NULL,
diff --git a/js/symb/collections.traitattr.js b/js/symb/collections.traitattr.js
index b028fbb1b1..4d2ee4c0cc 100644
--- a/js/symb/collections.traitattr.js
+++ b/js/symb/collections.traitattr.js
@@ -46,7 +46,7 @@ function traitChanged(elem){
 	var elemType =  elem.getAttribute("type");
 	var elemName = elem.getAttribute("name");
 	var traitID = elemName.substring(8,elemName.length-2);
-	$('input[name="stateid-'+traitID+'[]"]').each(function(){
+	$('input[name="traitid-'+traitID+'[]"]').each(function(){
 		if(this.checked == false){
 			//Uncheck children to match parent
 			$("input:checkbox.child-"+this.value).each(function(){ this.checked = false; });
@@ -63,7 +63,7 @@ function traitChanged(elem){
 	    }
 	}
 	if(!sessionStorage.attributeTree || sessionStorage.attributeTree == 0){
-		$('input[name="stateid-'+traitID+'[]"]').each(function(){
+		$('input[name="traitid-'+traitID+'[]"]').each(function(){
 			if((elemType == 'text' && elemType.value.trim() != '') || this.checked == true){
 				if(sessionStorage.attributeTree == 0) $("div.child-"+this.value).show();
 			}

From ec66d388d90960e6d93b7ad4346af19e194bff39 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Mon, 23 Sep 2019 21:49:48 -0700
Subject: [PATCH 15/23] Adjsutments to specimen upload

- Adjustment to image mapping imports to flush old images
- Add DwC paleo terms for mapping to symbiota paleo terms
- Fix bug that was skipping some id annotations that had blank annotator values
---
 classes/SpecUploadBase.php | 52 +++++++++++++++++++++++++++++---------
 1 file changed, 40 insertions(+), 12 deletions(-)

diff --git a/classes/SpecUploadBase.php b/classes/SpecUploadBase.php
index d3ae3c52dc..73108d04d1 100644
--- a/classes/SpecUploadBase.php
+++ b/classes/SpecUploadBase.php
@@ -145,6 +145,25 @@ public function loadFieldMap($autoBuildFieldMap = false){
 		//Add additional fields that are used for mapping to other fields just before record is imported into uploadspectemp
 		$this->symbFields[] = 'coordinateuncertaintyradius';
 		$this->symbFields[] = 'coordinateuncertaintyunits';
+		//Add DwC GeologicalContext (paleo) terms
+		$this->symbFields[] = 'geologicalcontextid';
+		$this->symbFields[] = 'earliestEonOrLowestEonothem';
+		$this->symbFields[] = 'latestEonOrHighestEonothem';
+		$this->symbFields[] = 'earliestEraOrLowestErathem';
+		$this->symbFields[] = 'latestEraOrHighestErathem';
+		$this->symbFields[] = 'earliestPeriodOrLowestSystem';
+		$this->symbFields[] = 'latestPeriodOrHighestSystem';
+		$this->symbFields[] = 'earliestEpochOrLowestSeries';
+		$this->symbFields[] = 'latestEpochOrHighestSeries';
+		$this->symbFields[] = 'earliestAgeOrLowestStage';
+		$this->symbFields[] = 'latestAgeOrHighestStage';
+		$this->symbFields[] = 'lowestBiostratigraphicZone';
+		$this->symbFields[] = 'highestBiostratigraphicZone';
+		$this->symbFields[] = 'lithostratigraphicTermsProperty';
+		$this->symbFields[] = 'group';
+		$this->symbFields[] = 'formation';
+		$this->symbFields[] = 'member';
+		$this->symbFields[] = 'bed';
 
 		switch ($this->uploadType) {
 			case $this->FILEUPLOAD:
@@ -970,7 +989,7 @@ private function prepareImages(){
 			$sql = 'DELETE FROM uploadimagetemp '.
 				'WHERE (originalurl LIKE "%.dng" OR originalurl LIKE "%.tif") AND (collid = '.$this->collId.')';
 			if($this->conn->query($sql)){
-				$this->outputMsg('<li style="margin-left:10px;">step 1 of 3... </li>');
+				$this->outputMsg('<li style="margin-left:10px;">step 1 of 5... </li>');
 			}
 			else{
 				$this->outputMsg('<li style="margin-left:20px;">WARNING removing non-jpgs from uploadimagetemp: '.$this->conn->error.'</li> ');
@@ -981,7 +1000,7 @@ private function prepareImages(){
 				'SET ui.occid = u.occid '.
 				'WHERE (ui.occid IS NULL) AND (u.occid IS NOT NULL) AND (ui.collid = '.$this->collId.')';
 			if($this->conn->query($sql)){
-				$this->outputMsg('<li style="margin-left:10px;">step 2 of 3... </li>');
+				$this->outputMsg('<li style="margin-left:10px;">step 2 of 5... </li>');
 			}
 			else{
 				$this->outputMsg('<li style="margin-left:20px;">WARNING updating occids within uploadimagetemp: '.$this->conn->error.'</li> ');
@@ -989,12 +1008,22 @@ private function prepareImages(){
 
 			//Remove previously loaded images where urls match exactly
 			$sql = 'DELETE u.* FROM uploadimagetemp u INNER JOIN images i ON u.occid = i.occid '.
-				'WHERE (u.collid = '.$this->collId.') AND (u.originalurl = i.originalurl)';
+				'WHERE (u.collid = '.$this->collId.') AND (u.originalurl = i.originalurl) AND (u.url = i.url)';
 			if($this->conn->query($sql)){
-				$this->outputMsg('<li style="margin-left:10px;">step 3 of 3... </li>');
+				$this->outputMsg('<li style="margin-left:10px;">step 3 of 5... </li>');
 			}
 			else{
-				$this->outputMsg('<li style="margin-left:20px;">ERROR deleting uploadimagetemp records with matching originalurls: '.$this->conn->error.'</li> ');
+				$this->outputMsg('<li style="margin-left:20px;">ERROR deleting uploadimagetemp records with matching urls: '.$this->conn->error.'</li> ');
+			}
+			if($this->collMetadataArr["managementtype"] == 'Snapshot'){
+				//Flush non-matching image derivatives (e.g. thumbnails)
+				$sql = 'DELETE i.* FROM uploadimagetemp u INNER JOIN images i ON u.occid = i.occid WHERE (i.collid = '.$this->collId.') AND (u.originalurl = i.originalurl)';
+				if($this->conn->query($sql)){
+					$this->outputMsg('<li style="margin-left:10px;">step 4 of 5... </li>');
+				}
+				else{
+					$this->outputMsg('<li style="margin-left:20px;">ERROR deleting image records with matching originalurls: '.$this->conn->error.'</li> ');
+				}
 			}
 			$sql = 'DELETE u.* FROM uploadimagetemp u INNER JOIN images i ON u.occid = i.occid '.
 				'WHERE (u.collid = '.$this->collId.') AND (u.url = i.url) AND (i.url != "") AND (i.url != "empty")';
@@ -1277,13 +1306,12 @@ protected function loadIdentificationRecord($recMap){
 					}
 				}
 
-				$sqlFragments = $this->getSqlFragments($recMap,$this->identFieldMap);
-				if($sqlFragments){
-					if($recMap['identifiedby'] || $recMap['dateidentified']){
-						if(!isset($recMap['identifiedby']) || !$recMap['identifiedby']) $recMap['identifiedby'] = 'not specified';
-						if(!isset($recMap['dateidentified']) || $recMap['dateidentified']) $recMap['dateidentified'] = 'not specified';
-						$sql = 'INSERT INTO uploaddetermtemp(collid'.$sqlFragments['fieldstr'].') '.
-							'VALUES('.$this->collId.$sqlFragments['valuestr'].')';
+				if($recMap['identifiedby'] || $recMap['dateidentified']){
+					if(!isset($recMap['identifiedby']) || !$recMap['identifiedby']) $recMap['identifiedby'] = 'not specified';
+					if(!isset($recMap['dateidentified']) || $recMap['dateidentified']) $recMap['dateidentified'] = 'not specified';
+					$sqlFragments = $this->getSqlFragments($recMap,$this->identFieldMap);
+					if($sqlFragments){
+						$sql = 'INSERT INTO uploaddetermtemp(collid'.$sqlFragments['fieldstr'].') VALUES('.$this->collId.$sqlFragments['valuestr'].')';
 						//echo "<div>SQL: ".$sql."</div>"; exit;
 
 						if($this->conn->query($sql)){

From 19d7b9fa428137414fe34d38a6038b3e584e18c9 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Mon, 23 Sep 2019 22:01:49 -0700
Subject: [PATCH 16/23] Minor bug to previous submit

---
 classes/SpecUploadBase.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/classes/SpecUploadBase.php b/classes/SpecUploadBase.php
index 73108d04d1..72c78f5478 100644
--- a/classes/SpecUploadBase.php
+++ b/classes/SpecUploadBase.php
@@ -1017,7 +1017,7 @@ private function prepareImages(){
 			}
 			if($this->collMetadataArr["managementtype"] == 'Snapshot'){
 				//Flush non-matching image derivatives (e.g. thumbnails)
-				$sql = 'DELETE i.* FROM uploadimagetemp u INNER JOIN images i ON u.occid = i.occid WHERE (i.collid = '.$this->collId.') AND (u.originalurl = i.originalurl)';
+				$sql = 'DELETE i.* FROM uploadimagetemp u INNER JOIN images i ON u.occid = i.occid WHERE (u.collid = '.$this->collId.') AND (u.originalurl = i.originalurl)';
 				if($this->conn->query($sql)){
 					$this->outputMsg('<li style="margin-left:10px;">step 4 of 5... </li>');
 				}

From f9ddc52d9d761a9279c8eae68e0a71537976d368 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Tue, 24 Sep 2019 00:55:30 -0700
Subject: [PATCH 17/23] Image Processing adjustments

- Extended verbatim coordinate parsing
- Minor adjustments to iPlant default processing start date
- Misc adjustments
---
 classes/ImageProcessor.php                 |  2 +-
 classes/SpecProcessorOcr.php               | 69 +++-------------------
 collections/editor/occurrenceeditor.php    |  2 +-
 collections/specprocessor/ocrprocessor.php | 56 +++++++++---------
 config/symbbase.php                        |  1 -
 js/symb/collections.occureditormain.js     | 33 +++++++++++
 6 files changed, 72 insertions(+), 91 deletions(-)

diff --git a/classes/ImageProcessor.php b/classes/ImageProcessor.php
index 3eecc85ba1..0bedf0b6d6 100644
--- a/classes/ImageProcessor.php
+++ b/classes/ImageProcessor.php
@@ -115,7 +115,7 @@ public function processIPlantImages($pmTerm, $postArr){
 				return false;
 			}
 			//Get start date
-			if(!$lastRunDate || !preg_match('/^\d{4}-\d{2}-\d{2}$/',$lastRunDate)) $lastRunDate = '2015-04-01';
+			if(!$lastRunDate || !preg_match('/^\d{4}-\d{2}-\d{2}$/',$lastRunDate)) $lastRunDate = '2019-05-01';
 			while(strtotime($lastRunDate) < strtotime('now')){
 				$url = $iPlantDataUrl.'image?value=*'.$iPlantSourcePath.'*&tag_query=upload_datetime:'.$lastRunDate.'*';
 				$contents = @file_get_contents($url);
diff --git a/classes/SpecProcessorOcr.php b/classes/SpecProcessorOcr.php
index 975f3e774b..5e967dc7b4 100644
--- a/classes/SpecProcessorOcr.php
+++ b/classes/SpecProcessorOcr.php
@@ -3,10 +3,10 @@
  * Used by automatic nightly process and by the occurrence editor (/collections/editor/occurrenceeditor.php)
  */
 include_once($SERVER_ROOT.'/config/dbconnection.php');
+include_once($SERVER_ROOT.'/classes/Manager.php');
 
-class SpecProcessorOcr{
+class SpecProcessorOcr extends Manager{
 
-	private $conn;
 	private $tempPath;
 	private $imgUrlLocal;
 	private $deleteAllOcrFiles = 0;
@@ -26,13 +26,13 @@ class SpecProcessorOcr{
 	private $errorStr;
 
 	function __construct() {
+		parent::__construct(null,'write');
 		$this->setTempPath();
-		$this->conn = MySQLiConnectionFactory::getCon("write");
 	}
 
 	function __destruct(){
+		parent::__destruct();
 		if($this->logFH) fclose($this->logFH);
- 		if(!($this->conn === false)) $this->conn->close();
 		//unlink($this->imgUrlLocal);
 	}
 
@@ -91,20 +91,20 @@ private function ocrImageByUrl($imgUrl,$getBest = 0,$sciName=''){
 	}
 
 	private function ocrImage($url = ""){
-		global $tesseractPath;
+		global $TESSERACT_PATH;
 		$retStr = '';
 		if(!$url) $url = $this->imgUrlLocal;
 		if($url){
 			//OCR image, result text is output to $outputFile
 			$output = array();
 			$outputFile = substr($url,0,strlen($url)-4);
-			if(isset($tesseractPath) && $tesseractPath){
-				if(substr($tesseractPath,0,2) == 'C:'){
+			if(isset($TESSERACT_PATH) && $TESSERACT_PATH){
+				if(substr($TESSERACT_PATH,0,2) == 'C:'){
 					//Full path to tesseract with quotes needed for Windows
-					exec('"'.$tesseractPath.'" '.$url.' '.$outputFile,$output);
+					exec('"'.$TESSERACT_PATH.'" '.$url.' '.$outputFile,$output);
 				}
 				else{
-					exec($tesseractPath.' '.$url.' '.$outputFile,$output);
+					exec($TESSERACT_PATH.' '.$url.' '.$outputFile,$output);
 				}
 			}
 			else{
@@ -858,56 +858,5 @@ private function cleanRawStr($inStr){
 		);
 		return $retStr;
 	}
-
-	private function encodeString($inStr){
-		global $CHARSET;
-		$retStr = $inStr;
-		//Get rid of Windows curly (smart) quotes
-		$search = array(chr(145),chr(146),chr(147),chr(148),chr(149),chr(150),chr(151));
-		$replace = array("'","'",'"','"','*','-','-');
-		$inStr = str_replace($search, $replace, $inStr);
-		//Get rid of UTF-8 curly smart quotes and dashes
-		$badwordchars=array("\xe2\x80\x98", // left single quote
-							"\xe2\x80\x99", // right single quote
-							"\xe2\x80\x9c", // left double quote
-							"\xe2\x80\x9d", // right double quote
-							"\xe2\x80\x94", // em dash
-							"\xe2\x80\xa6" // elipses
-		);
-		$fixedwordchars=array("'", "'", '"', '"', '-', '...');
-		$inStr = str_replace($badwordchars, $fixedwordchars, $inStr);
-
-		if($inStr){
-			if(strtolower($CHARSET) == "utf-8" || strtolower($CHARSET) == "utf8"){
-				if(mb_detect_encoding($inStr,'UTF-8,ISO-8859-1',true) == "ISO-8859-1"){
-					$retStr = utf8_encode($inStr);
-					//$retStr = iconv("ISO-8859-1//TRANSLIT","UTF-8",$inStr);
-				}
-			}
-			elseif(strtolower($CHARSET) == "iso-8859-1"){
-				if(mb_detect_encoding($inStr,'UTF-8,ISO-8859-1') == "UTF-8"){
-					$retStr = utf8_decode($inStr);
-					//$retStr = iconv("UTF-8","ISO-8859-1//TRANSLIT",$inStr);
-				}
-			}
-			//$line = iconv('macintosh', 'UTF-8', $line);
-			//mb_detect_encoding($buffer, 'windows-1251, macroman, UTF-8');
- 		}
-		return $retStr;
-	}
-
-	private function cleanOutStr($str){
-		$newStr = str_replace('"',"&quot;",$str);
-		$newStr = str_replace("'","&apos;",$newStr);
-		//$newStr = $this->conn->real_escape_string($newStr);
-		return $newStr;
-	}
-
-	private function cleanInStr($str){
-		$newStr = trim($str);
-		$newStr = preg_replace('/\s\s+/', ' ',$newStr);
-		$newStr = $this->conn->real_escape_string($newStr);
-		return $newStr;
-	}
 }
 ?>
\ No newline at end of file
diff --git a/collections/editor/occurrenceeditor.php b/collections/editor/occurrenceeditor.php
index 5e645a17bb..1818d6d413 100644
--- a/collections/editor/occurrenceeditor.php
+++ b/collections/editor/occurrenceeditor.php
@@ -476,7 +476,7 @@ function requestImage(){
 	</script>
 	<script src="../../js/symb/collections.coordinateValidation.js?ver=170310" type="text/javascript"></script>
 	<script src="../../js/symb/wktpolygontools.js?ver=180208" type="text/javascript"></script>
-	<script src="../../js/symb/collections.occureditormain.js?ver=201904" type="text/javascript"></script>
+	<script src="../../js/symb/collections.occureditormain.js?ver=201909" type="text/javascript"></script>
 	<script src="../../js/symb/collections.occureditortools.js?ver=1909" type="text/javascript"></script>
 	<script src="../../js/symb/collections.occureditorimgtools.js?ver=170310" type="text/javascript"></script>
 	<script src="../../js/jquery.imagetool-1.7.js?ver=140310" type="text/javascript"></script>
diff --git a/collections/specprocessor/ocrprocessor.php b/collections/specprocessor/ocrprocessor.php
index 8011541345..7c064ef530 100644
--- a/collections/specprocessor/ocrprocessor.php
+++ b/collections/specprocessor/ocrprocessor.php
@@ -22,14 +22,14 @@
 				modal: true,
 				position: { my: "left top", at: "right bottom", of: "#"+dialogStr }
 			});
-	
+
 			$( "#"+dialogStr ).click(function() {
 				$( "#"+this.id+"dialog" ).dialog( "open" );
 			});
 		}
-	
+
 	});
-	
+
 	function validateStatQueryForm(f){
 		if(f.pscrit.value == ""){
 			alert("Please select a processing status");
@@ -45,7 +45,7 @@ function validateOcrTessForm(f){
 		}
 		return true;
 	}
-	
+
 	function validateOcrUploadForm(f){
 		if(f.speckeypattern.value == ""){
 			alert("Please enter a pattern matching string for extracting the catalog number");
@@ -68,7 +68,7 @@ function validateOcrUploadForm(f){
 	}
 </script>
 <div style="margin:15px;">
-	<?php 
+	<?php
 	$cntTotal = $procManager->getSpecWithImage();
 	$cntUnproc = $procManager->getSpecWithImage($procStatus);
 	$cntUnprocNoOcr = $procManager->getSpecNoOcr($procStatus);
@@ -76,12 +76,12 @@ function validateOcrUploadForm(f){
 	?>
 	<fieldset style="padding:20px;">
 		<legend><b>Specimen Image Statistics</b></legend>
-		
-		<div><b>Total specimens with images:</b> <?php echo $cntTotal; ?></div> 
-		<div><b>&quot;<?php echo $procStatus; ?>&quot; specimens with images:</b> <?php echo $cntUnproc; ?></div> 
+
+		<div><b>Total specimens with images:</b> <?php echo $cntTotal; ?></div>
+		<div><b>&quot;<?php echo $procStatus; ?>&quot; specimens with images:</b> <?php echo $cntUnproc; ?></div>
 		<div style="margin-left:15px;">with OCR: <?php echo ($cntUnproc-$cntUnprocNoOcr); ?></div>
 		<div style="margin-left:15px;">without OCR: <?php echo $cntUnprocNoOcr; ?> </div>
-		
+
 		<div style="margin:15px">
 			<b>Custom Query: </b><br/>
 			<form name="statqueryform" action="index.php" method="post" onsubmit="return validateStatQueryForm(this)">
@@ -89,7 +89,7 @@ function validateOcrUploadForm(f){
 					<option value="">Select Processing Status</option>
 					<option value="">-----------------------------------</option>
 					<option value="null">No Status</option>
-					<?php 
+					<?php
 					$psList = $procManager->getProcessingStatusList();
 					foreach($psList as $psVal){
 						echo '<option value="'.$psVal.'">'.$psVal.'</option>';
@@ -106,16 +106,16 @@ function validateOcrUploadForm(f){
 	<fieldset style="padding:20px;margin-top:20px;">
 		<legend><b>Batch OCR Images using the Tesseract OCR Engine</b></legend>
 		<?php
-		if(isset($tesseractPath) && $tesseractPath){ 
+		if(isset($TESSERACT_PATH) && $TESSERACT_PATH){
 			?>
 			<form name="batchTessform" action="processor.php" method="post" onsubmit="return validateBatchTessForm(this)">
 				<div style="padding:3px;">
-					<b>Processing Status:</b> 
+					<b>Processing Status:</b>
 					<select name="procstatus">
 						<option value="unprocessed">unprocessed</option>
 						<option value="">-----------------------------------</option>
 						<option value="null">No Status</option>
-						<?php 
+						<?php
 						$psList = $procManager->getProcessingStatusList();
 						foreach($psList as $psVal){
 							if($psVal != 'unprocessed'){
@@ -126,7 +126,7 @@ function validateOcrUploadForm(f){
 					</select><br/>
 				</div>
 				<div style="padding:3px;">
-					<b>Number of records to process:</b> 
+					<b>Number of records to process:</b>
 					<input name="batchlimit" type="text" value="100" style="width:60px" />
 				</div>
 				<div style="padding:15px;">
@@ -144,8 +144,8 @@ function validateOcrUploadForm(f){
 			echo '<div style="margin:25px"><b>';
 			echo 'The Tesseract OCR engine does not appear to be installed or the tesseractPath variable is not set within the Symbiota configuration file. ';
 			echo 'Contact your system administrator to resolve these issues. ';
-			echo '</b></div>'; 
-		} 
+			echo '</b></div>';
+		}
 		?>
 	</fieldset>
 
@@ -153,9 +153,9 @@ function validateOcrUploadForm(f){
 		<legend><b>OCR Batch Import Tool</b></legend>
 		<form name="ocruploadform" action="processor.php" method="post" enctype="multipart/form-data" onsubmit="return validateOcrUploadForm(this);">
 			<div style="margin:15px">
-				This interface will upload OCR text files generated outside of the portal environment. 
-				For instance, ABBYY FineReader has the ability to batch OCR specimen images and output the results as separate text files (.txt) named after the source image. 
-				OCR text files are linked to specimen records by matching catalog numbers extracted from the file name and comparing OCR and iamge file names.   
+				This interface will upload OCR text files generated outside of the portal environment.
+				For instance, ABBYY FineReader has the ability to batch OCR specimen images and output the results as separate text files (.txt) named after the source image.
+				OCR text files are linked to specimen records by matching catalog numbers extracted from the file name and comparing OCR and iamge file names.
 			</div>
 			<div style="margin:15px">
 				<b>Requirements:</b>
@@ -165,7 +165,7 @@ function validateOcrUploadForm(f){
 					<li>Files must be named using the Catalog Number. The regular expression below will be used to extract catalog number from file name. Click information symbol for more information.</li>
 					<li>Since OCR text needs to be linked to source image, images must have been previously uploaded into portal</li>
 					<li>If there are more than one image linked to a specimen, the full file name will be used to determine which image to link the OCR</li>
-				</ul> 
+				</ul>
 			</div>
 			<div style="margin:15px">
 				<table style="width:100%;">
@@ -180,16 +180,16 @@ function validateOcrUploadForm(f){
 							</a>
 							<div id="speckeypatterninfodialog">
 								Regular expression needed to extract the unique identifier from source text.
-								For example, regular expression /^(WIS-L-\d{7})\D*/ will extract catalog number WIS-L-0001234 
+								For example, regular expression /^(WIS-L-\d{7})\D*/ will extract catalog number WIS-L-0001234
 								from image file named WIS-L-0001234_a.jpg. For more information on creating regular expressions,
 								Google &quot;Regular Expression PHP Tutorial&quot;. It is recommended to have the portal manager
-								help with the initial setup of batch processing.  
+								help with the initial setup of batch processing.
 							</div>
 						</td>
 					</tr>
 					<tr>
 						<td>
-							<b>Zip file containing OCR:</b> 
+							<b>Zip file containing OCR:</b>
 						</td>
 						<td>
 							<div style="float:right;"><a href="#" onclick="toggle('pathElem');return false;" title="toggle option to enter full path">full path option</a></div>
@@ -203,14 +203,14 @@ function validateOcrUploadForm(f){
 									Browse and select zip file that contains the multiple OCR text files.
 								</div>
 							</div>
-							<div class="pathElem" style="display:none;"> 
+							<div class="pathElem" style="display:none;">
 								<input name="sourcepath" type="text" style="width:350px;" value="<?php echo $procManager->getSourcePath(); ?>" />
 								<a id="sourcepathinfo" href="#" onclick="return false" title="More Information">
 									<img src="../../images/info.png" style="width:15px;" />
 								</a>
 								<div id="sourcepathinfodialog">
 									File path or URL to folder containing the OCR text files.
-									If a URL (e.g. http://) is supplied, the web server needs to be configured to list 
+									If a URL (e.g. http://) is supplied, the web server needs to be configured to list
 									all files within the directory, or the html output needs to list all images in anchor tags.
 									Scripts will attempt to crawl through all child directories.
 								</div>
@@ -219,9 +219,9 @@ function validateOcrUploadForm(f){
 					</tr>
 					<tr>
 						<td>
-							<b>OCR Source:</b> 
+							<b>OCR Source:</b>
 						</td>
-						<td> 
+						<td>
 							<input name="ocrsource" type="text" value="" />
 							<a id="ocrsourceinfo" href="#" onclick="return false" title="More Information">
 								<img src="../../images/info.png" style="width:15px;" />
@@ -236,7 +236,7 @@ function validateOcrUploadForm(f){
 							<input name="title" type="hidden" value="OCR Harvest" />
 							<input name="newprofile" type="hidden" value="<?php echo ($procManager->getSpecKeyPattern()?'0':'1'); ?>" />
 							<input name="spprid" type="hidden" value="<?php echo $spprid; ?>" />
-							<input name="collid" type="hidden" value="<?php echo $collid; ?>" /> 
+							<input name="collid" type="hidden" value="<?php echo $collid; ?>" />
 							<input name="tabindex" type="hidden" value="3" />
 							<div style="margin:25px">
 								<input name="submitaction" type="submit" value="Load OCR Files" />
diff --git a/config/symbbase.php b/config/symbbase.php
index ff9518d66f..3e685610cf 100644
--- a/config/symbbase.php
+++ b/config/symbbase.php
@@ -116,7 +116,6 @@
 if(!isset($imgLgWidth) && isset($IMG_LG_WIDTH)) $imgLgWidth = $IMG_LG_WIDTH;
 if(!isset($imgFileSizeLimit) && isset($IMG_FILE_SIZE_LIMIT)) $imgFileSizeLimit = $IMG_FILE_SIZE_LIMIT;
 if(!isset($useImageMagick) && isset($USE_IMAGE_MAGICK)) $useImageMagick = $USE_IMAGE_MAGICK;
-if(!isset($tesseractPath) && isset($TESSERACT_PATH)) $tesseractPath = $TESSERACT_PATH;
 if(!isset($occurrenceModIsActive) && isset($OCCURRENCE_MOD_IS_ACTIVE)) $occurrenceModIsActive = $OCCURRENCE_MOD_IS_ACTIVE;
 if(!isset($floraModIsActive) && isset($FLORA_MOD_IS_ACTIVE)) $floraModIsActive = $FLORA_MOD_IS_ACTIVE;
 if(!isset($keyModIsActive) && isset($KEY_MOD_IS_ACTIVE)) $keyModIsActive = $KEY_MOD_IS_ACTIVE;
diff --git a/js/symb/collections.occureditormain.js b/js/symb/collections.occureditormain.js
index 1671a4f974..93214005bf 100644
--- a/js/symb/collections.occureditormain.js
+++ b/js/symb/collections.occureditormain.js
@@ -507,6 +507,7 @@ function parseVerbatimCoordinates(f,verbose){
 		if(!latDec || !lngDec){
 			var llEx1 = /(\d{1,2})[\D\s]{1,2}(\d{1,2}\.{0,1}\d*)['m]{1}\s*(\d{1,2}\.{0,1}\d*)['"s]{1,2}\s*([NS]{0,1})[\D\s]*(\d{1,3})[\D\s]{1,2}(\d{1,2}\.{0,1}\d*)['m]{1}\s*(\d{1,2}\.{0,1}\d*)['"s]{1,2}\s*([EW]{0,1})/i 
 			var llEx2 = /(\d{1,2})[\D\s]{1,2}(\d{1,2}\.{0,1}\d*)['m]{1}\s*([NS]{0,1})\D*\s*(\d{1,3})[\D\s]{1,2}(\d{1,2}\.{0,1}\d*)['m]{1}\s*([EW]{0,1})/i 
+			var llEx3 = /([-]{0,1}\d{1,2}\.\d+)[\s]{0,1}([NSEW]{0,1})[\s]+([-]{0,1}\d{1,3}\.\d+)[\s]{0,1}([NSEW]{0,1})/i 
 			if(extractArr = llEx1.exec(verbCoordStr)){
 				var latDeg = parseInt(extractArr[1]);
 				var latMin = parseInt(extractArr[2]);
@@ -571,6 +572,38 @@ function parseVerbatimCoordinates(f,verbose){
 				if((extractArr[3] == "S" || extractArr[3] == "s") && latDec > 0) latDec = latDec*-1;
 				if(lngDec > 0 && extractArr[6] != "E" && extractArr[6] != "e") lngDec = lngDec*-1;
 			}
+			else if(extractArr = llEx3.exec(verbCoordStr)){
+				var latDec = parseFloat(extractArr[1]);
+				var latNS = extractArr[2].toUpperCase();
+				
+				var lngDec = parseFloat(extractArr[3]);
+				var lngEW = extractArr[4].toUpperCase();
+				
+				if((latNS == "E" || latNS == "W") && (lngEW == "N" || lngEW == "S")){
+					var tempDec = lngDec;
+					var tempHemi = lngEW;
+					lngDec = latDec;
+					lngEW = latNS;
+					latDec = tempDec;
+					latNS = tempHemi;
+				}
+				if(latNS != ""){
+					if(latNS != "N" && latNS != "S" && lngEW != "E" && lngEW != "W"){
+						alert("Invalid hemisphere designations (allowed: N, S, E, W");
+						return '';
+					}
+				}
+				if(latDec > 0 && latNS == "S") latDec = -1*latDec;
+				if(lngDec > 0 && lngEW == "W") lngDec = -1*lngDec;
+				if(latDec > 90 || latDec < -90){
+					alert("Latitude must be between -90 and 90");
+					return '';
+				}
+				if(lngDec > 180 || lngDec < -180){
+					alert("Longitude must be between -180 and 180");
+					return '';
+				}
+			}
 		}
 
 		if(latDec && lngDec){

From abef8cbc5e24f9181bea00cdaaa71dac20511d24 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Tue, 24 Sep 2019 09:46:48 -0700
Subject: [PATCH 18/23] OCR bug

- Fatal error due to imcomplete integration of manager class into OCR tools
---
 classes/SpecProcessorOcr.php              | 115 ++++++++--------------
 collections/specprocessor/ocr_handler.php |  10 +-
 collections/specprocessor/processor.php   |   4 +-
 3 files changed, 47 insertions(+), 82 deletions(-)

diff --git a/classes/SpecProcessorOcr.php b/classes/SpecProcessorOcr.php
index 5e967dc7b4..633160aeab 100644
--- a/classes/SpecProcessorOcr.php
+++ b/classes/SpecProcessorOcr.php
@@ -20,11 +20,6 @@ class SpecProcessorOcr extends Manager{
 	private $specKeyPattern;
 	private $ocrSource;
 
-	//If silent is set, script will produce no non-fatal output.
-	private $verbose = 0;			//0 = silent, 1 = logFile, 2 = echo, 3 = both
-	private $logFH;
-	private $errorStr;
-
 	function __construct() {
 		parent::__construct(null,'write');
 		$this->setTempPath();
@@ -32,7 +27,6 @@ function __construct() {
 
 	function __destruct(){
 		parent::__destruct();
-		if($this->logFH) fclose($this->logFH);
 		//unlink($this->imgUrlLocal);
 	}
 
@@ -78,13 +72,13 @@ private function ocrImageByUrl($imgUrl,$getBest = 0,$sciName=''){
 			}
 			else{
 				$err = 'ERROR: Unable to load image, URL: '.$imgUrl;
-				$this->logMsg($err,1);
+				$this->logOrEcho($err,1);
 				$rawStr = 'ERROR';
 			}
 		}
 		else{
 			$err = 'ERROR: Empty URL';
-			$this->logMsg($err,1);
+			$this->logOrEcho($err,1);
 			$rawStr = 'ERROR';
 		}
 		return $rawStr;
@@ -124,7 +118,7 @@ private function ocrImage($url = ""){
 				unlink($outputFile.'.txt');
 			}
 			else{
-				$this->logMsg("ERROR: Unable to locate output file",1);
+				$this->logOrEcho("ERROR: Unable to locate output file",1);
 			}
 		}
 		return $retStr;//$this->cleanRawStr($retStr);
@@ -144,8 +138,8 @@ private function databaseRawStr($imgId,$rawStr,$notes,$source){
 				return true;
 			}
 			else{
-				$this->logMsg("ERROR: Unable to load fragment into database: ".$this->conn->error,1);
-				$this->logMsg("SQL: ".$sql,2);
+				$this->logOrEcho("ERROR: Unable to load fragment into database: ".$this->conn->error,1);
+				$this->logOrEcho("SQL: ".$sql,2);
 				return false;
 			}
 		}
@@ -198,7 +192,7 @@ public function batchOcrUnprocessed($inCollStr,$procStatus = 'unprocessed',$limi
 
 			//Batch OCR
 			foreach($collArr as $collid => $instCode){
-				$this->logMsg('Starting batch processing for '.$instCode);
+				$this->logOrEcho('Starting batch processing for '.$instCode);
 				$sql = 'SELECT i.imgid, IFNULL(i.originalurl, i.url) AS url, o.sciName, i.occid '.
 					'FROM omoccurrences o INNER JOIN images i ON o.occid = i.occid '.
 					'LEFT JOIN specprocessorrawlabels r ON i.imgid = r.imgid '.
@@ -210,7 +204,7 @@ public function batchOcrUnprocessed($inCollStr,$procStatus = 'unprocessed',$limi
 					while($r = $rs->fetch_object()){
 						$rawStr = $this->ocrImageByUrl($r->url,$getBest,$r->sciName);
 						if($rawStr != 'ERROR'){
-							$this->logMsg('#'.$recCnt.': image <a href="../editor/occurrenceeditor.php?occid='.$r->occid.'" target="_blank">'.$r->imgid.'</a> processed ('.date("Y-m-d H:i:s").')');
+							$this->logOrEcho('#'.$recCnt.': image <a href="../editor/occurrenceeditor.php?occid='.$r->occid.'" target="_blank">'.$r->imgid.'</a> processed ('.date("Y-m-d H:i:s").')');
 							$notes = '';
 							$source = 'Tesseract: '.date('Y-m-d');
 							$this->databaseRawStr($r->imgid,$rawStr,$notes,$source);
@@ -233,8 +227,8 @@ public function harvestOcrText($postArr){
 		$this->ocrSource = $postArr['ocrsource'];
 		$this->specKeyPattern = $postArr['speckeypattern'];
 		if(!$this->specKeyPattern){
-			$this->errorStr = 'ERROR loading OCR files: Specimen catalog number pattern missing';
-			$this->logMsg($this->errorStr);
+			$this->errorMessage = 'ERROR loading OCR files: Specimen catalog number pattern missing';
+			$this->logOrEcho($this->errorMessage);
 			return false;
 		}
 		$sourcePath = '';
@@ -246,38 +240,38 @@ public function harvestOcrText($postArr){
 			$sourcePath = $this->uploadOcrFile();
 		}
 		if(!$sourcePath){
-			$this->errorStr = 'ERROR loading OCR files: OCR source path is missing';
-			$this->logMsg($this->errorStr);
+			$this->errorMessage = 'ERROR loading OCR files: OCR source path is missing';
+			$this->logOrEcho($this->errorMessage);
 			return false;
 		}
 		if(substr($sourcePath,0,4) == 'http'){
 			//http protocol, thus test for a valid page
 			$headerArr = get_headers($sourcePath);
 			if(!$headerArr){
-				$this->errorStr = 'ERROR loading OCR files: sourcePath returned bad headers ('.$sourcePath.')';
-				$this->logMsg($this->errorStr);
+				$this->errorMessage = 'ERROR loading OCR files: sourcePath returned bad headers ('.$sourcePath.')';
+				$this->logOrEcho($this->errorMessage);
 				return false;
 			}
 			preg_match('/http.+\s{1}(\d{3})\s{1}/i',$headerArr[0],$codeArr);
 			if($codeArr[1] == '403'){
-				$this->errorStr = 'ERROR loading OCR files: sourcePath returned Forbidden ('.$sourcePath.')';
-				$this->logMsg($this->errorStr);
+				$this->errorMessage = 'ERROR loading OCR files: sourcePath returned Forbidden ('.$sourcePath.')';
+				$this->logOrEcho($this->errorMessage);
 				return false;
 			}
 			if($codeArr[1] == '404'){
-				$this->errorStr = 'ERROR loading OCR files: sourcePath returned a page Not Found error ('.$sourcePath.')';
-				$this->logMsg($this->errorStr);
+				$this->errorMessage = 'ERROR loading OCR files: sourcePath returned a page Not Found error ('.$sourcePath.')';
+				$this->logOrEcho($this->errorMessage);
 				return false;
 			}
 			if($codeArr[1] != '200'){
-				$this->errorStr = 'ERROR loading OCR files: sourcePath returned error code '.$codeArr[1].' ('.$sourcePath.')';
-				$this->logMsg($this->errorStr);
+				$this->errorMessage = 'ERROR loading OCR files: sourcePath returned error code '.$codeArr[1].' ('.$sourcePath.')';
+				$this->logOrEcho($this->errorMessage);
 				return false;
 			}
 		}
 		elseif(!file_exists($sourcePath)){
-			$this->errorStr = 'ERROR loading OCR files: sourcePath does not exist ('.$sourcePath.')';
-			$this->logMsg($this->errorStr);
+			$this->errorMessage = 'ERROR loading OCR files: sourcePath does not exist ('.$sourcePath.')';
+			$this->logOrEcho($this->errorMessage);
 			return false;
 		}
 		//Initiate processing
@@ -288,7 +282,7 @@ public function harvestOcrText($postArr){
 		else{
 			$this->processOcrFolder($sourcePath);
 		}
-		$this->logMsg('Done loading OCR files ');
+		$this->logOrEcho('Done loading OCR files ');
 
 
 		return $status;
@@ -297,13 +291,13 @@ public function harvestOcrText($postArr){
 	private function uploadOcrFile(){
 		$retPath = '';
 		if(!array_key_exists('ocrfile',$_FILES)){
-			$this->errorStr = 'ERROR loading OCR file: OCR file missing';
-			$this->logMsg($this->errorStr);
+			$this->errorMessage = 'ERROR loading OCR file: OCR file missing';
+			$this->logOrEcho($this->errorMessage);
 			return ;
 		}
 		if(!$this->tempPath){
-			$this->errorStr = 'ERROR loading OCR file: temp target path empty';
-			$this->logMsg($this->errorStr);
+			$this->errorMessage = 'ERROR loading OCR file: temp target path empty';
+			$this->logOrEcho($this->errorMessage);
 			return ;
 		}
 		$zipPath = $this->tempPath.'ocrupload.zip';
@@ -321,14 +315,14 @@ private function uploadOcrFile(){
 				unlink($zipPath);
 			}
 			else{
-				$this->errorStr = 'ERROR unpacking OCR file: '.$res;
-				$this->logMsg($this->errorStr);
+				$this->errorMessage = 'ERROR unpacking OCR file: '.$res;
+				$this->logOrEcho($this->errorMessage);
 				return ;
 			}
 		}
 		else{
-			$this->errorStr = 'ERROR loading OCR file: input file lacks zip extension';
-			$this->logMsg($this->errorStr);
+			$this->errorMessage = 'ERROR loading OCR file: input file lacks zip extension';
+			$this->logOrEcho($this->errorMessage);
 			return ;
 		}
 		return $retPath;
@@ -344,16 +338,16 @@ private function processOcrHtml($sourcePath){
 			if(!in_array($fileName,$skipAnchors)){
 				$fileExt = strtolower(substr($fileName,strrpos($fileName,'.')+1));
 				if($fileExt){
-					$this->logMsg("Processing OCR File: ".$fileName);
+					$this->logOrEcho("Processing OCR File: ".$fileName);
 					if($fileExt == "txt"){
 						$this->processOcrFile($fileName,$sourcePath);
 					}
 					else{
-						$this->logMsg("ERROR: File skipped, not a supported OCR file with .txt extension: ".$sourcePath.$fileName);
+						$this->logOrEcho("ERROR: File skipped, not a supported OCR file with .txt extension: ".$sourcePath.$fileName);
 					}
 				}
 				elseif(stripos($fileName,'Parent Dir') === false){
-					$this->logMsg('New dir path: '.$sourcePath.$fileName);
+					$this->logOrEcho('New dir path: '.$sourcePath.$fileName);
 					$this->processOcrHtml($sourcePath.$fileName.'/');
 				}
 			}
@@ -367,13 +361,13 @@ private function processOcrFolder($sourcePath){
 			while($fileName = readdir($dirFH)){
 				if($fileName != "." && $fileName != ".." && $fileName != ".svn"){
 					if(is_file($sourcePath.$fileName)){
-						$this->logMsg("Processing OCR File: ".$fileName);
+						$this->logOrEcho("Processing OCR File: ".$fileName);
 						$fileExt = strtolower(substr($fileName,strrpos($fileName,'.')));
 						if($fileExt == ".txt"){
 							$this->processOcrFile($fileName,$sourcePath);
 						}
 						else{
-							$this->logMsg("ERROR: File skipped, not a supported OCR text file (.txt): ".$fileName);
+							$this->logOrEcho("ERROR: File skipped, not a supported OCR text file (.txt): ".$fileName);
 						}
 					}
 					elseif(is_dir($sourcePath.$fileName)){
@@ -384,14 +378,14 @@ private function processOcrFolder($sourcePath){
 			if($dirFH) closedir($dirFH);
 		}
 		else{
-			$this->logMsg("ERROR: unable to access source directory: ".$sourcePath,1);
+			$this->logOrEcho("ERROR: unable to access source directory: ".$sourcePath,1);
 		}
 		if($this->deleteAllOcrFiles) unlink($sourcePath);
 	}
 
 	private function processOcrFile($fileName,$sourcePath){
 		$ocrCnt = 0;
-		//$this->logMsg('Starting OCR text processing... ',1);
+		//$this->logOrEcho('Starting OCR text processing... ',1);
 		if($rawTextFH = fopen($sourcePath.$fileName, 'r')){
 			$rawStr = fread($rawTextFH, filesize($sourcePath.$fileName));
 			fclose($rawTextFH);
@@ -451,15 +445,15 @@ private function processOcrFile($fileName,$sourcePath){
 					}
 				}
 				else{
-					$this->logMsg('ERROR: unable locate specimen image (catalog #: '.$catNumber.')',1);
+					$this->logOrEcho('ERROR: unable locate specimen image (catalog #: '.$catNumber.')',1);
 				}
 			}
 			else{
-				$this->logMsg('ERROR: unable to extract catalog number ('.$fileName.' using '.$this->specKeyPattern.')',1);
+				$this->logOrEcho('ERROR: unable to extract catalog number ('.$fileName.' using '.$this->specKeyPattern.')',1);
 			}
 		}
 		else{
-			$this->logMsg('ERROR: unable to read rawOcr file: '.$fileName,1);
+			$this->logOrEcho('ERROR: unable to read rawOcr file: '.$fileName,1);
 		}
 	}
 
@@ -600,7 +594,7 @@ private function getBestOCR($sciName = ''){
 		$score_treated = $this->scoreOCR($rawStr_treated, $sciName);
 		unlink($urlTemp);
 		if($score_treated > $score_base) {
-			$this->logMsg('Best Score applied',1);
+			$this->logOrEcho('Best Score applied',1);
 			return $rawStr_treated;
 		} else {
 			return $rawStr_base;
@@ -770,20 +764,6 @@ public function setCropH($h){
 		$this->cropH = $h;
 	}
 
-	public function getErrorStr(){
-		return $this->errorStr;
-	}
-
-	public function setVerbose($s){
-		$this->verbose = $s;
-		if($this->verbose == 1 || $this->verbose == 3){
-			if($this->tempPath){
-				$logPath = $this->tempPath.'log_'.date('Ymd').'.log';
-				$this->logFH = fopen($logPath, 'a');
-			}
-		}
-	}
-
 	private function setTempPath(){
 		$tempPath = 0;
 		if(array_key_exists('tempDirRoot',$GLOBALS)){
@@ -810,19 +790,6 @@ private function setTempPath(){
 	}*/
 
 	//Misc functions
-	private function logMsg($msg,$indent = 0) {
-		if($this->verbose == 1 || $this->verbose == 3){
-			if($this->logFH){
-				$msg .= "\n";
-				if($indent) $msg = "\t".$msg;
-				fwrite($this->logFH, $msg);
-			}
-		}
-		elseif($this->verbose > 1 ){
-			echo '<li style="margin-left:'.($indent*15).'px">'.$msg.'</li>';
-		}
-	}
-
 	private function cleanRawStr($inStr){
 		$retStr = $this->encodeString($inStr);
 
diff --git a/collections/specprocessor/ocr_handler.php b/collections/specprocessor/ocr_handler.php
index 995da5c460..6f8d72c325 100644
--- a/collections/specprocessor/ocr_handler.php
+++ b/collections/specprocessor/ocr_handler.php
@@ -1,6 +1,6 @@
 <?php
 //This file can be triggered by a CRON job for automatci OCR of unprocessed images
-//Following example OCR collection ids 1,4, and 5. Script will also out to log file  
+//Following example OCR collection ids 1,4, and 5. Script will also out to log file
 //php ocr_handler.php '1,4,5' 0
 include_once('../../config/symbini.php');
 include_once($SERVER_ROOT.'/classes/SpecProcessorOcr.php');
@@ -9,14 +9,12 @@
 $collStr = '';
 if(array_key_exists(1,$argv)){
 	$collStr = $argv[1];
-} 
+}
 if(array_key_exists(2,$argv)){
 	$silect = $argv[2];
-} 
+}
 
 $ocrManager = new SpecProcessorOcr();
-$ocrManager->setSilent($silent);		//Turn on logging
-
+$ocrManager->setVerboseMode($silent);
 $ocrManager->batchOcrUnprocessed($collStr);
-
 ?>
\ No newline at end of file
diff --git a/collections/specprocessor/processor.php b/collections/specprocessor/processor.php
index 1ef6704259..3d1b4ffa70 100644
--- a/collections/specprocessor/processor.php
+++ b/collections/specprocessor/processor.php
@@ -127,7 +127,7 @@
 				}
 				elseif($action == 'Run Batch OCR'){
 					$ocrManager = new SpecProcessorOcr();
-					$ocrManager->setVerbose(2);
+					$ocrManager->setVerboseMode(2);
 					$batchLimit = 100;
 					if(array_key_exists('batchlimit',$_POST)) $batchLimit = $_POST['batchlimit'];
 					echo '<ul>';
@@ -137,7 +137,7 @@
 				elseif($action == 'Load OCR Files'){
 					$specManager->addProject($_POST);
 					$ocrManager = new SpecProcessorOcr();
-					$ocrManager->setVerbose(2);
+					$ocrManager->setVerboseMode(2);
 					echo '<ul>';
 					$ocrManager->harvestOcrText($_POST);
 					echo '</ul>';

From d651f369ee164060d936300da69bab6b19cf31d5 Mon Sep 17 00:00:00 2001
From: Andrew Johnston <ajohnston@asu.edu>
Date: Tue, 24 Sep 2019 16:02:36 -0700
Subject: [PATCH 19/23] Increased font sizes on the checklist display page,
 changed voucher text size and indent

---
 checklists/checklist.php | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/checklists/checklist.php b/checklists/checklist.php
index 625166afbe..5cf83a9b1f 100644
--- a/checklists/checklist.php
+++ b/checklists/checklist.php
@@ -697,15 +697,17 @@
 							$group = $sppArr['taxongroup'];
 							if($group != $prevGroup){
 								$famUrl = '../taxa/index.php?taxauthid=1&taxon='.strip_tags($group).'&clid='.$clid;
+								//Edit family name display style here
 								?>
-								<div class="familydiv" id="<?php echo strip_tags($group);?>" style="margin:12px 0px 3px 0px;font-weight:bold;">
+								<div class="familydiv" id="<?php echo strip_tags($group);?>" style="margin:12px 0px 3px 0px;font-weight:bold;font-size:150%;">
 									<a href="<?php echo $famUrl; ?>" target="_blank" style="color:black;"><?php echo $group;?></a>
 								</div>
 								<?php
 								$prevGroup = $group;
 							}
 							echo "<div id='tid-$tid' style='margin:0px 0px 3px 10px;'>";
-							echo '<div style="clear:left">';
+							//Edit species name display style here
+							echo '<div style="clear:left;font-size:130%;">';
 							if(!preg_match('/\ssp\d/',$sppArr["sciname"])) echo '<a href="../taxa/index.php?taxauthid=1&taxon='.$tid.'&clid='.$clid.'" target="_blank">';
 							echo "<b><i>".$sppArr["sciname"]."</b></i> ";
 							if(array_key_exists("author",$sppArr)) echo $sppArr["author"];
@@ -770,7 +772,8 @@
 									$noteStr = $sppArr['notes'];
 								}
 								if($noteStr || $voucStr){
-									echo "<div style='margin-left:15px;'>".$noteStr.($noteStr && $voucStr?'; ':'').$voucStr."</div>";
+								//Edit notes and voucher display style here
+									echo "<div style='margin-left:25px;font-size:95%;'>".$noteStr.($noteStr && $voucStr?'; ':'').$voucStr."</div>";
 								}
 							}
 							echo "</div>\n";

From a0a0c62e5dddf46150f21fcf9233c2071d845a16 Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Wed, 25 Sep 2019 09:40:50 -0700
Subject: [PATCH 20/23] Image Mapping debugging

- Bug fix that blocked loading multiple image when only large image version is supplied without a web derivative
- Bug fix that blocked loading when extra non-mapped column are included in the upload file.
---
 classes/ImageProcessor.php                   |  7 ++++++-
 collections/specprocessor/imageprocessor.php | 20 ++++++++++++--------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/classes/ImageProcessor.php b/classes/ImageProcessor.php
index 0bedf0b6d6..c650e54828 100644
--- a/classes/ImageProcessor.php
+++ b/classes/ImageProcessor.php
@@ -374,7 +374,12 @@ public function loadFileData($postArr){
 								while($r1 = $rs1->fetch_object()){
 									$uFileName = substr(strrchr($r1->url, "/"), 1);
 									$oFileName = substr(strrchr($r1->originalurl, "/"), 1);
-									if($oFileName == $origFileName || $uFileName == $urlFileName || $oFileName == $urlFileName || $uFileName == $origFileName){
+									$replaceImg = false;
+									if($oFileName && $oFileName == $origFileName) $replaceImg = true;
+									elseif($uFileName && $uFileName == $urlFileName) $replaceImg = true;
+									elseif($oFileName && $oFileName == $urlFileName) $replaceImg = true;
+									elseif($uFileName && $uFileName == $origFileName) $replaceImg = true;
+									if($replaceImg){
 										$sql2 = 'UPDATE images '.
 											'SET url = "'.$url.'", originalurl = "'.$originalUrl.'", thumbnailurl = '.($thumbnailUrl?'"'.$thumbnailUrl.'"':'NULL').', '.
 											'sourceurl = '.($sourceUrl?'"'.$sourceUrl.'"':'NULL').' '.
diff --git a/collections/specprocessor/imageprocessor.php b/collections/specprocessor/imageprocessor.php
index 77058a9c8a..a671e0d3fc 100644
--- a/collections/specprocessor/imageprocessor.php
+++ b/collections/specprocessor/imageprocessor.php
@@ -197,18 +197,22 @@ function validateFileUploadForm(f){
 				for(var i=0;i<f.length;i++){
 					var obj = f.elements[i];
 					if(obj.name.indexOf("tf[") == 0){
-						if(tfArr.indexOf(obj.value) > -1){
-							alert("ERROR: Target field names must be unique (duplicate field: "+obj.value+")");
-							return false;
+						if(obj.value){
+							if(tfArr.indexOf(obj.value) > -1){
+								alert("ERROR: Target field names must be unique (duplicate field: "+obj.value+")");
+								return false;
+							}
+							tfArr[tfArr.length] = obj.value;
 						}
-						tfArr[tfArr.length] = obj.value;
 					}
 					if(obj.name.indexOf("sf[") == 0){
-						if(sfArr.indexOf(obj.value) > -1){
-							alert("ERROR: Source field names must be unique (duplicate field: "+obj.value+")");
-							return false;
+						if(obj.value){
+							if(sfArr.indexOf(obj.value) > -1){
+								alert("ERROR: Source field names must be unique (duplicate field: "+obj.value+")");
+								return false;
+							}
+							sfArr[sfArr.length] = obj.value;
 						}
-						sfArr[sfArr.length] = obj.value;
 					}
 				}
 				if(tfArr.indexOf("catalognumber") < 0 && tfArr.indexOf("othercatalognumbers") < 0){

From d12347268d8a4ebf351061dbacd9e20e53e366ab Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Wed, 25 Sep 2019 23:39:39 -0700
Subject: [PATCH 21/23] Checklist Development

- Added class tags to checklist elements
- Moved inline styling into external base.css
---
 checklists/checklist.php |  23 +--
 config/symbbase.php      |   2 +-
 css/base.css             | 324 ++++++++++++++++++++-------------------
 css/main_template.css    | 177 ++++++---------------
 index_template.php       |   9 ++
 5 files changed, 236 insertions(+), 299 deletions(-)

diff --git a/checklists/checklist.php b/checklists/checklist.php
index 5cf83a9b1f..6b7b4a83b1 100644
--- a/checklists/checklist.php
+++ b/checklists/checklist.php
@@ -153,12 +153,12 @@
 		#sddm div{position: absolute;visibility:hidden;margin:0;padding:0;background:#EAEBD8;border:1px solid #5970B2}
 		#sddm div a	{position: relative;display:block;margin:0;padding:5px 10px;width:auto;white-space:nowrap;text-align:left;text-decoration:none;background:#EAEBD8;color:#2875DE;font-weight:bold;}
 		#sddm div a:hover{background:#49A3FF;color:#FFF}
+
 		<?php
 		if($printMode){
 			?>
 			body{ background-color:#ffffff;  }
 			#innertext{ background-color:#ffffff; }
-			#taxaDiv{ line-height: 1em; }
 			.printoff{ display:none; }
 			a{ color: currentColor; cursor: none; pointer-events: none; text-decoration: none; }
 			<?php
@@ -689,7 +689,7 @@
 					}
 					else{
 						//Display taxa
-						echo '<div id="taxaDiv">';
+						echo '<div id="taxalist-div">';
 						$voucherArr = array();
 						if($showVouchers) $voucherArr = $clManager->getVoucherArr();
 						$prevGroup = '';
@@ -699,27 +699,27 @@
 								$famUrl = '../taxa/index.php?taxauthid=1&taxon='.strip_tags($group).'&clid='.$clid;
 								//Edit family name display style here
 								?>
-								<div class="familydiv" id="<?php echo strip_tags($group);?>" style="margin:12px 0px 3px 0px;font-weight:bold;font-size:150%;">
+								<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 = $group;
 							}
-							echo "<div id='tid-$tid' style='margin:0px 0px 3px 10px;'>";
+							echo '<div id="tid-'.$tid.'" class="taxon-container">';
 							//Edit species name display style here
-							echo '<div style="clear:left;font-size:130%;">';
+							echo '<div class="taxon-div">';
 							if(!preg_match('/\ssp\d/',$sppArr["sciname"])) echo '<a href="../taxa/index.php?taxauthid=1&taxon='.$tid.'&clid='.$clid.'" target="_blank">';
-							echo "<b><i>".$sppArr["sciname"]."</b></i> ";
+							echo '<span class="taxon-span">'.$sppArr['sciname'].'</span> ';
 							if(array_key_exists("author",$sppArr)) echo $sppArr["author"];
 							if(!preg_match('/\ssp\d/',$sppArr["sciname"])) echo "</a>";
 							if(array_key_exists('vern',$sppArr)){
-								echo " - <span style='font-weight:bold;'>".$sppArr["vern"]."</span>";
+								echo ' - <span class="vern-span">'.$sppArr['vern'].'</span>';
 							}
 							$clidArr = array();
 							if(isset($sppArr['clid'])) $clidArr = explode(',',$sppArr['clid']);
 							if($clArray["dynamicsql"]){
 								?>
-								<span class="printoff" style="margin:0px 10px">
+								<span class="view-specimen-span printoff">
 									<a href="../collections/list.php?usethes=1&taxontype=2&taxa=<?php echo $tid."&targetclid=".$clid."&targettid=".$tid;?>" target="_blank">
 										<img src="../images/list.png" style="width:12px;" title="<?php echo (isset($LANG['VIEW_RELATED'])?$LANG['VIEW_RELATED']:'View Related Specimens'); ?>" />
 									</a>
@@ -749,7 +749,7 @@
 							}
 							echo "</div>\n";
 							if($showSynonyms && isset($sppArr['syn'])){
-								echo '<div style="margin-left:15px">['.$sppArr['syn'].']</div>';
+								echo '<div class="syn-div">['.$sppArr['syn'].']</div>';
 							}
 							if($showVouchers){
 								$voucStr = '';
@@ -773,7 +773,7 @@
 								}
 								if($noteStr || $voucStr){
 								//Edit notes and voucher display style here
-									echo "<div style='margin-left:25px;font-size:95%;'>".$noteStr.($noteStr && $voucStr?'; ':'').$voucStr."</div>";
+									echo '<div class="note-div">'.$noteStr.($noteStr && $voucStr?'; ':'').$voucStr.'</div>';
 								}
 							}
 							echo "</div>\n";
@@ -783,7 +783,8 @@
 					$taxaLimit = ($showImages?$clManager->getImageLimit():$clManager->getTaxaLimit());
 					if($clManager->getTaxaCount() > (($pageNumber)*$taxaLimit)){
 						echo '<div class="printoff" style="margin:20px;clear:both;">';
-						echo '<a href="checklist.php?pagenumber='.($pageNumber+1).$argStr.'"> '.$LANG['DISPLAYNEXT'].' '.$taxaLimit.' '.$LANG['TAXA'].'...</a></div>';
+						echo '<a href="checklist.php?pagenumber='.($pageNumber+1).$argStr.'"> '.$LANG['DISPLAYNEXT'].' '.$taxaLimit.' '.$LANG['TAXA'].'...</a>';
+						echo '</div>';
 					}
 					if(!$taxaArray) echo "<h1 style='margin:40px;'>".$LANG['NOTAXA']."</h1>";
 					?>
diff --git a/config/symbbase.php b/config/symbbase.php
index 3e685610cf..c50d12636e 100644
--- a/config/symbbase.php
+++ b/config/symbbase.php
@@ -55,7 +55,7 @@
     $USER_RIGHTS = $_SESSION['userrights'];
 }
 
-$CSS_VERSION = '9';
+$CSS_VERSION = '10';
 $USER_DISPLAY_NAME = (array_key_exists("dn",$PARAMS_ARR)?$PARAMS_ARR["dn"]:"");
 $USERNAME = (array_key_exists("un",$PARAMS_ARR)?$PARAMS_ARR["un"]:0);
 $SYMB_UID = (array_key_exists("uid",$PARAMS_ARR)?$PARAMS_ARR["uid"]:0);
diff --git a/css/base.css b/css/base.css
index 995e009a40..c4321a1cac 100644
--- a/css/base.css
+++ b/css/base.css
@@ -1,12 +1,18 @@
-/* Do not modify styles within this file
- * Instead, modify styles within the main.css file to override the default styles within this file 
- * 
- **/
+/*
+ * Do not modify styles within this file
+ * Instead, modify styles within the main.css file to override the default styles declared within this file 
+*/
 body{
+	width: 80%;
+	min-width:1000px;
 	margin:	8px;
+	margin-top:0px;
 	margin-left: auto;
 	margin-right: auto;
-	font-size: 12px;
+	background-color: #FFFFFF;
+	color: #000000;
+	font-size: 1em;
+	font-family: Arial, Helvetica, sans-serif;
 }
 
 /*Main table framework*/
@@ -79,64 +85,6 @@ span[class=link]:hover {
     text-decoration: underline;	
 }
 
-/* General Image thumbnails   */
-div.tndiv{
-	float: left;
-	text-align: center;
-	width: 165px;
-	height: 230px;
-	page-break-before:auto;
-	page-break-inside:avoid;
-}
-
-div.tnimg{
-	position: relative;
-	overflow:	hidden;
-	width:	160px;
-	height:	160px;
-	border:	1px solid gray;
-}
-
-div.tnimg a{
-
-}
-
-div.tnimg img{
-	position: absolute;
-	max-height: 160px;
-	max-width: 160px;
-	width: 		expression(this.width >= this.height ? 160: true);
-	height:		expression(this.height >= this.width ? 160: true);
-	top: -9999px;
-	bottom: -9999px;
-	left: -9999px;
-	right: -9999px;
-	margin: auto;
-}	
-
-/* styled table */
-
-table.styledtable{
-	width:				100%; 
-	border-collapse:	collapse; 
-}
-table.styledtable th {
-	text-align:			left; 
-	padding:			4px;
-	border:				1px solid gray; 
-	background-color:	#dbe5f1; 
-	color:				black; 
-}
-table.styledtable td {
-	padding:		3px;
-	border:			1px solid gray; 
-	background-color: #efefef;
-}
-table.styledtable tr.alt td {
-	color:				#000000; 
-	/*background-color:	#FCFCFC; */
-	background-color: #dfdfdf;
-}
 
 /*  navpath styles */
 div.navpath {
@@ -154,62 +102,113 @@ div.navpath a:hover {
 	font-size: 11px;
 }
 
-/*Download buttons on the search display pages*/
-div.button {
-	background-color:	#FFFFD7;
-	padding:			3px;
-	border:				1px outset #A0A0A0;
+/* /collections/ folder pages */
+.collectiontable{
+	float: left;
 }
 
-div.button img {
-	border:	0px;	
+.collectiontable td{
+	vertical-align: middle;
 }
 
-div.button:hover {
-	border:	1px inset #A0A0A0;
+.categorytitle{ 
 }
 
-/*Dynamic Key module*/
-#keytable{
+.categorytitle a{ 
+	font-weight: bold; 
+	font-size:	110%;
+}
 
+.collectiontitle{
+	font-size:12px;
+	margin-top:8px;
 }
 
-#keycharcolumn{
-	vertical-align:	top;
-	width:	30%;
+.collectiontitle a{
+	font-size: 80%;
+	margin-left: 3px;
 }
 
-#keymidcolumn {
-	width:	20px;
+.collectiontitle a:hover{
+	font-weight: bold;
+	color: grey;
 }
 
-#keytaxacolumn{
-	vertical-align:	top;
-	width:	65%;
+.collectionname{
+	float:left;
+	font-weight: bold;
+	margin-left: 3px;
 }
 
-.charHeading{
+.collectioncode{
+	float:left;
+	margin-left: 3px;
+}
 
+#omlisttable{
+	 width:	90%;
 }
 
-.characterStateName{
+#omlisttable img{
+    border: medium double #990000;
+}
 
+.nextbtn {
+	font-weight: bold,
+	background-color: #dddddd;
+	border-color: #999;
+    color: black;
+	width: 110px;
+	padding: 5px 8px;
+	border-radius: 5px;
 }
 
-.dynam{
+.nextbtn:hover {
+	background: #e5f1fd;
+	color: black;
+}
 
+.resetbtn {
+	font-weight: bold,
+	background-color: #c0c0c0;
+	border-color: #999;
+    color: black;
+	width: 90px;
+	padding: 4px 6px;
+	border-radius: 2px;
 }
 
-.dynamlang{
-	margin-top:0.5em;
-	font-weight: bold;
+.resetbtn:hover {
+	background-color: #e5f1fd;
+    color: black;
 }
 
-.dynamopt{
+/*Download buttons on the search display pages*/
+div.button {
+	background-color:	#FFFFD7;
+	padding:			3px;
+	border:				1px outset #A0A0A0;
+}
 
+div.button img {
+	border:	0px;	
+}
+
+div.button:hover {
+	border:	1px inset #A0A0A0;
 }
 
-/* misc page specific items */
+/* Species list component */
+#taxalist-div{ line-height: 1em; }
+.family-div{ margin:20px 0px 10px 0px; font-weight:bold; }
+.taxon-container{ margin:0px 0px 8px 10px; }
+.taxon-div{ clear:left; margin-bottom: 5px; }
+.taxon-span{ font-weight: bold; font-style: italic }
+.vern-span{ font-weight:bold; }
+.view-specimen-span{ margin:0px 10px }
+.syn-div{ margin-left:15px }
+.note-div{ margin-left:25px; font-size:95%; }
+
 #cloptiondiv{
 	margin:		5px;
 	width:		250px;
@@ -218,9 +217,6 @@ div.button:hover {
 	max-width: 20% !important;
 	min-height:	325px;
 }
-#img-container {
-	width: 80%;
-}
 
 #taxonfilterdiv{
 	padding:			5px;
@@ -232,65 +228,107 @@ div.button:hover {
 	 margin:	3px;
 }
 
+#img-container {
+	width: 80%;
+}
+
+/*Dynamic Key module*/
+#keytable{
 
-/* /collections/ folder pages */
-.collectiontable{
-	float: left;
 }
 
-.collectiontable td{
-	vertical-align: middle;
+#keycharcolumn{
+	vertical-align:	top;
+	width:	30%;
 }
 
-.categorytitle{ 
+#keymidcolumn {
+	width:	20px;
 }
 
-.categorytitle a{ 
-	font-weight: bold; 
-	font-size:	110%;
+#keytaxacolumn{
+	vertical-align:	top;
+	width:	65%;
 }
 
-.collectiontitle{
-	font-size:12px;
-	margin-top:8px;
+.charHeading{
+
 }
 
-.collectiontitle a{
-	font-size: 80%;
-	margin-left: 3px;
+.characterStateName{
+
 }
 
-.collectiontitle a:hover{
-	font-weight: bold;
-	color: grey;
+.dynam{
+
 }
 
-.collectionname{
-	float:left;
+.dynamlang{
+	margin-top:0.5em;
 	font-weight: bold;
-	margin-left: 3px;
 }
 
-.collectioncode{
-	float:left;
-	margin-left: 3px;
+.dynamopt{
+
 }
 
-#omlisttable{
-	 width:	90%;
+/* General Image thumbnails   */
+div.tndiv{
+	float: left;
+	text-align: center;
+	width: 165px;
+	height: 230px;
+	page-break-before:auto;
+	page-break-inside:avoid;
 }
 
-#omlisttable img{
-    border: medium double #990000;
+div.tnimg{
+	position: relative;
+	overflow:	hidden;
+	width:	160px;
+	height:	160px;
+	border:	1px solid gray;
 }
 
-/* Slideshow Plugin */
-#slideshowcontainer{
-	border: 2px solid black;
-	border-radius:10px;
-	padding:10px;
-	margin-left: auto;
-	margin-right: auto;
+div.tnimg a{
+
+}
+
+div.tnimg img{
+	position: absolute;
+	max-height: 160px;
+	max-width: 160px;
+	width: 		expression(this.width >= this.height ? 160: true);
+	height:		expression(this.height >= this.width ? 160: true);
+	top: -9999px;
+	bottom: -9999px;
+	left: -9999px;
+	right: -9999px;
+	margin: auto;
+}	
+
+
+/* styled table */
+table.styledtable{
+	width:				100%; 
+	border-collapse:	collapse; 
+}
+table.styledtable th {
+	text-align:			left; 
+	padding:			4px;
+	border:				1px solid gray; 
+	background-color:	#dbe5f1; 
+	color:				black; 
+}
+table.styledtable td {
+	padding:		3px;
+	border:			1px solid gray; 
+	background-color: #efefef;
+}
+table.styledtable tr.alt td {
+	color:				#000000; 
+	/*background-color:	#FCFCFC; */
+	background-color: #dfdfdf;
 }
 
 /* misc */
@@ -305,36 +343,6 @@ div.genericpopup{
 	border:					black solid 3px;
 }
 
-.nextbtn {
-	font-weight: bold,
-	background-color: #dddddd;
-	border-color: #999;
-    color: black;
-	width: 110px;
-	padding: 5px 8px;
-	border-radius: 5px;
-}
-
-.nextbtn:hover {
-	background: #e5f1fd;
-	color: black;
-}
-
-.resetbtn {
-	font-weight: bold,
-	background-color: #c0c0c0;
-	border-color: #999;
-    color: black;
-	width: 90px;
-	padding: 4px 6px;
-	border-radius: 2px;
-}
-
-.resetbtn:hover {
-	background-color: #e5f1fd;
-    color: black;
-}
-
 /* JQuery Manifest alterations */
 div.mf_container {
 	border: 1px solid #aaa;
diff --git a/css/main_template.css b/css/main_template.css
index 87f8fb5cb0..137b0c52f8 100644
--- a/css/main_template.css
+++ b/css/main_template.css
@@ -1,108 +1,21 @@
-/* Modify styles within this file to override styles within base.css file 
+/* Modify styles within this file to override styles deinfed within base.css file 
  * 
  **/
-body{
-	width: 80%;
-	min-width:950px;
-	margin-top:0px;
-	background-color: #FFFFFF;
-	color: #000000;
-	font-family: Arial, Helvetica, sans-serif;
-	font-size: 12px;
-}
+body{ }
 
 /*Main table framework*/
-#maintable{
-	width: 100%;
-	background-color:#FFFFFF;
-	border:1px solid #333333;
-}
-
-#maintable td{
-
-}
-
-#header{
-	text-align:left;
-	padding:0px;
-}
-
-#header a{
-
-}
-
-#header a:hover{
-
-}
-
-#middleleft{
-}
-
-#middleleftnomenu{
-}
-
-#middlecenter{
-	padding:0px;
-	font-family: Arial, Helvetica, sans-serif;
-	font-size: 12px;
-}
-
-#middleright{
-}
-
-#footer{
-}
-
-/*Central div in the middle center table div */
-#innertext{
-	font-family: Arial, Helvetica, sans-serif;
-	font-size: 12px;
-}
-
-#innertext a{
-
-}
-#innertext a:hover{
-
-}
-
-div.navpath {
-}
-
-/* Image thumbnails   */
-div.tndiv{
-
-}
-
-div.tnimg{
-
-}
-
-div.tnimg a{
-
-}
-
-div.tnimg img{
-
-}	
-
-/*Misc general items*/
-table{
-
-}
-
-h1{
-
-}
-
-h2{
-
-}
-
-h3{
-
-}
-
+#maintable{  }
+#maintable td{  }
+#header{  }
+#header a{  }
+#header a:hover{  }
+#middleleft{  }
+#middleleftnomenu{  }
+#middlecenter{  }
+#middleright{ }
+#footer{  }
+
+/* Header menu items */
 #top_navbar{
 	clear:both;
 	height:33px;
@@ -194,46 +107,52 @@ h3{
 	background:#999999; 
 }
 
-.categorytitle{
-}
 
-.categorytitle a{ 
-}
+div.navpath {  }
 
-.collectiontitle{
-}
-
-.collectiontitle a{
+/*Central div in the middle center table div */
+#innertext{
+	font-family: Arial, Helvetica, sans-serif;
+	font-size: 12px;
 }
 
-.collectiontitle a:hover{
-}
+#innertext a{
 
-.collectionname{
 }
+#innertext a:hover{
 
-.collectioncode{
 }
 
+.categorytitle{ }
+.categorytitle a{  }
 
-#omlisttable{
-	 font-size: 12px;
-}
-
+.collectiontitle{ }
+.collectiontitle a{ }
+.collectiontitle a:hover{ }
+.collectionname{ }
+.collectioncode{ }
 
-/* Quick Search Plugin */
-#quicksearchdiv{
-}
+#omlisttable{ }
 
-#quicksearchtext{
-}
+/* Species list component */
+#taxalist-div{  }
+.family-div{  }
+.taxon-container{  }
+.taxon-div{  }
+.taxon-span{  }
+.vern-span{  }
+.view-specimen-span{  }
+.syn-div{  }
+.note-div{  }
 
-#quicksearchtaxon{
-}
+#cloptiondiv{  }
+#taxonfilterdiv{  }
+#taxonfilterdiv{  }
+#img-container {  }
 
-#quicksearchbutton{
-}
 
-/* Slideshow Plugin */
-#slideshowcontainer{
-}
\ No newline at end of file
+/* Image thumbnails   */
+div.tndiv{ }
+div.tnimg{ }
+div.tnimg a{ }
+div.tnimg img{ }	
diff --git a/index_template.php b/index_template.php
index dc313998c0..fa8e86c36c 100644
--- a/index_template.php
+++ b/index_template.php
@@ -16,6 +16,15 @@
 	<script type="text/javascript">
 		<?php include_once($SERVER_ROOT.'/config/googleanalytics.php'); ?>
 	</script>
+	<style>
+		#slideshowcontainer{
+			border: 2px solid black;
+			border-radius:10px;
+			padding:10px;
+			margin-left: auto;
+			margin-right: auto;
+		}
+	</style>
 </head>
 <body>
 	<?php

From d19a32134165896a61efe4d52aac49d5e4bb2dea Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Thu, 26 Sep 2019 12:53:59 -0700
Subject: [PATCH 22/23] Image Maintenance Tools

- Bug fix that was returning wrong image dimensions during specific situations
---
 classes/ImageShared.php | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/classes/ImageShared.php b/classes/ImageShared.php
index 0833313148..d7f98db9ce 100644
--- a/classes/ImageShared.php
+++ b/classes/ImageShared.php
@@ -1237,11 +1237,11 @@ public static function getImgDim($imgUrl){
 	// Retrieve JPEG width and height without downloading/reading entire image.
 	private static function getImgDim1($imgUrl) {
 		$opts = array(
-				'http'=>array(
-						'user_agent' => $GLOBALS['DEFAULT_TITLE'],
-						'method'=>"GET",
-						'header'=> implode("\r\n", array('Content-type: text/plain;'))
-				)
+			'http'=>array(
+				'user_agent' => $GLOBALS['DEFAULT_TITLE'],
+				'method'=>"GET",
+				'header'=> implode("\r\n", array('Content-type: text/plain;'))
+			)
 		);
 		$context = stream_context_create($opts);
 		if($handle = fopen($imgUrl, "rb", false, $context)){
@@ -1263,9 +1263,14 @@ private static function getImgDim1($imgUrl) {
 								$sof_marker = array("\xC0", "\xC1", "\xC2", "\xC3", "\xC5", "\xC6", "\xC7", "\xC8", "\xC9", "\xCA", "\xCB", "\xCD", "\xCE", "\xCF");
 								if(in_array($new_block[$i+1], $sof_marker)) {
 									// SOF marker detected. Width and height information is contained in bytes 4-7 after this byte.
-									$size_data = $new_block[$i+2] . $new_block[$i+3] . $new_block[$i+4] . $new_block[$i+5] . $new_block[$i+6] . $new_block[$i+7] . $new_block[$i+8];
+									//$size_data = $new_block[$i+2] . $new_block[$i+3] . $new_block[$i+4] . $new_block[$i+5] . $new_block[$i+6] . $new_block[$i+7] . $new_block[$i+8];
+									$size_data = null;
+									for($x = 2; $x < 9; $x++){
+										if(isset($new_block[$i+$x])) $size_data .= $new_block[$i+$x];
+									}
 									$unpacked = unpack("H*", $size_data);
 									$unpacked = $unpacked[1];
+									if(!is_array($unpacked) || count($unpacked) < 13) return false;
 									$height = hexdec($unpacked[6] . $unpacked[7] . $unpacked[8] . $unpacked[9]);
 									$width = hexdec($unpacked[10] . $unpacked[11] . $unpacked[12] . $unpacked[13]);
 									return array($width, $height);

From 4fe1ea3cd2c7046a3b149b0eb0484e8fb61e68ae Mon Sep 17 00:00:00 2001
From: Edward Gilbert <egbot@asu.edu>
Date: Thu, 26 Sep 2019 15:47:43 -0700
Subject: [PATCH 23/23] Taxonomic Cleaning bug

- Extra spaces being place within animalia infraspecific names
---
 classes/TaxonomyHarvester.php | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/classes/TaxonomyHarvester.php b/classes/TaxonomyHarvester.php
index 34b4922595..7bfdb48edc 100644
--- a/classes/TaxonomyHarvester.php
+++ b/classes/TaxonomyHarvester.php
@@ -293,7 +293,7 @@ private function getColNode($nodeArr){
 		if(isset($nodeArr['infraspecies'])) $taxonArr['unitname3'] = $nodeArr['infraspecies'];
 		if(isset($nodeArr['infraspecies_marker'])){
 			$taxonArr['unitind3'] = $nodeArr['infraspecies_marker'];
-			$taxonArr['sciname'] = trim($taxonArr['unitname1'].' '.$taxonArr['unitname2'].' '.$taxonArr['unitind3'].' '.$taxonArr['unitname3']);
+			$taxonArr['sciname'] = trim($taxonArr['unitname1'].' '.$taxonArr['unitname2'].($taxonArr['unitind3']?' '.$taxonArr['unitind3']:'').' '.$taxonArr['unitname3']);
 		}
 		if(isset($nodeArr['author'])) $taxonArr['author'] = $nodeArr['author'];
 		if(isset($nodeArr['source_database'])) $taxonArr['source'] = $nodeArr['source_database'];