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Hotfix 2023 06 03 (BioKIC#508)
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* Occurrence Upload adjustment
    - Trim off delimiters that are left on the beginning or end of filter string to ensure that null values are not included
* Collection Listing bug fix
    - Collection categories failing to be persist
* Occurrence Image Submissions issue resolution
    - Set default image sort order to 40 for observations to ensure that preserved specimen images do not take precedence
* Image Processing bug
    - collection identifier (collid) failed to be passed to statistics update function
* Resolve Taxonomy Harvester issues
    - Improve TROPICOS method of matching on infraspecific taxa
    - Improve close match suggestions
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@egbot
egbot authored Jun 16, 2023
1 parent 091676d commit c79fe50
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Showing 6 changed files with 61 additions and 38 deletions.
6 changes: 2 additions & 4 deletions classes/ImageProcessor.php
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Original file line number Diff line number Diff line change
Expand Up @@ -347,8 +347,7 @@ public function loadFileData($postArr){
$occurMain = new OccurrenceMaintenance($this->conn);

$this->logOrEcho('Updating statistics...');
$occurMain->setCollidStr($this->collid);
if(!$occurMain->updateCollectionStatsBasic()){
if(!$occurMain->updateCollectionStatsBasic($this->collid)){
$errorArr = $occurMain->getErrorArr();
foreach($errorArr as $errorStr){
$this->logOrEcho($errorStr,1);
Expand Down Expand Up @@ -561,8 +560,7 @@ private function cleanHouse($collList){
if($collList){
$this->logOrEcho('Updating collection statistics...',2);
foreach($collList as $collid){
$occurMain->setCollidStr($collid);
if(!$occurMain->updateCollectionStatsBasic()){
if(!$occurMain->updateCollectionStatsBasic($collid)){
$errorArr = $occurMain->getErrorArr();
foreach($errorArr as $errorStr){
$this->logOrEcho($errorStr,1);
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1 change: 1 addition & 0 deletions classes/OccurrenceEditorImages.php
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Original file line number Diff line number Diff line change
Expand Up @@ -401,6 +401,7 @@ public function addImage($postArr){
if(array_key_exists('copyright',$postArr)) $imgManager->setCopyright($postArr['copyright']);
if(array_key_exists('notes',$postArr)) $imgManager->setNotes($postArr['notes']);
if(array_key_exists('sortoccurrence',$postArr)) $imgManager->setSortOccurrence($postArr['sortoccurrence']);
if(strpos($this->collMap['colltype'], 'Observations') !== false) $imgManager->setSortSeq(40);

$sourceImgUri = $postArr['imgurl'];
if($sourceImgUri){
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4 changes: 3 additions & 1 deletion classes/OccurrenceSearchSupport.php
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,9 @@ public function outputFullCollArr($collGrpArr, $targetCatID = '', $displayIcons
<td style="width:25px;">
<div style="">
<?php
$catSelected = !$catSelArr || in_array($catid, $catSelArr);
$catSelected = false;
if(!$catSelArr && !$collSelArr) $catSelected = true;
elseif(in_array($catid, $catSelArr)) $catSelected = true;
echo '<input data-role="none" id="cat-'.$idStr.'-Input" name="cat[]" value="'.$catid.'" type="checkbox" onclick="selectAllCat(this,\'cat-'.$idStr.'\')" '.($catSelected?'checked':'').' />';
?>
</div>
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2 changes: 1 addition & 1 deletion classes/SpecUploadBase.php
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Original file line number Diff line number Diff line change
Expand Up @@ -1961,7 +1961,7 @@ protected function setUploadTargetPath(){

public function addFilterCondition($columnName, $condition, $value){
if($columnName && ($value || $condition == 'ISNULL' || $condition == 'NOTNULL')){
$this->filterArr[strtolower($columnName)][$condition][] = strtolower(trim($value));
$this->filterArr[strtolower($columnName)][$condition][] = strtolower(trim($value,'; '));
}
}

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84 changes: 53 additions & 31 deletions classes/TaxonomyHarvester.php
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Original file line number Diff line number Diff line change
Expand Up @@ -785,7 +785,7 @@ private function addTropicosTaxon($taxonArr){
$sciName = str_replace(array(' subsp.',' ssp.',' var.',' f.'), '', $sciName);
$sciName = str_replace('.','', $sciName);
$sciName = str_replace(' ','%20', $sciName);
$url = 'http://services.tropicos.org/Name/Search?type='.$searchType.'&format=json&name='.$sciName.'&apikey='.$this->taxonomicResources['tropicos'];
$url = 'https://services.tropicos.org/Name/Search?type='.$searchType.'&format=json&name='.$sciName.'&apikey='.$this->taxonomicResources['tropicos'];
if($fh = fopen($url, 'r')){
$content = "";
while($line = fread($fh, 1024)){
Expand All @@ -794,14 +794,27 @@ private function addTropicosTaxon($taxonArr){
fclose($fh);
$resultArr = json_decode($content,true);
$id = 0;
$closeMatchArr = array();
foreach($resultArr as $arr){
$unitSciname = $arr['ScientificName'];
if(strpos($unitSciname, ' fo. ')) $unitSciname = str_replace(' fo. ', ' f. ', $unitSciname);
if(array_key_exists('Error', $arr)){
$this->logOrEcho('Taxon not found (code:1)',2);
return;
}
if(!array_key_exists('NomenclatureStatusID', $arr) || $arr['NomenclatureStatusID'] == 1){
$id = $arr['NameId'];
break;
if($taxonArr['sciname'] != $unitSciname){
$pattern = '/^\D+\s{1}\D+\s{1}(subsp|ssp|var|f)\.\s{1}\D+$/';
if(preg_match($pattern, $taxonArr['sciname'])){
if(preg_match($pattern, $unitSciname)){
$closeMatchArr[] = $arr['NameId'];
}
}
}
else{
if(!array_key_exists('NomenclatureStatusID', $arr) || $arr['NomenclatureStatusID'] == 1){
$id = $arr['NameId'];
break;
}
}
}
if($id){
Expand All @@ -810,6 +823,11 @@ private function addTropicosTaxon($taxonArr){
}
else{
$this->logOrEcho('Taxon not found (code:2)',2);
if($closeMatchArr){
foreach($closeMatchArr as $closeID){
$this->addTropicosTaxonByID($closeID);
}
}
}
}
else{
Expand All @@ -820,7 +838,7 @@ private function addTropicosTaxon($taxonArr){

private function addTropicosTaxonByID($id){
$taxonArr= Array();
$url = 'http://services.tropicos.org/Name/'.$id.'?apikey='.$this->taxonomicResources['tropicos'].'&format=json';
$url = 'https://services.tropicos.org/Name/'.$id.'?apikey='.$this->taxonomicResources['tropicos'].'&format=json';
if($fh = fopen($url, 'r')){
$content = "";
while($line = fread($fh, 1024)){
Expand All @@ -835,7 +853,7 @@ private function addTropicosTaxonByID($id){
$taxonArr['parent']['tid'] = 'self';
}
else{
$url = 'http://services.tropicos.org/Name/'.$id.'/HigherTaxa?apikey='.$this->taxonomicResources['tropicos'].'&format=json';
$url = 'https://services.tropicos.org/Name/'.$id.'/HigherTaxa?apikey='.$this->taxonomicResources['tropicos'].'&format=json';
if($fh = fopen($url, 'r')){
$content = '';
while($line = fread($fh, 1024)){
Expand All @@ -859,7 +877,7 @@ private function addTropicosTaxonByID($id){
//Get accepted name
$acceptedTid = 0;
if($taxonArr['acceptedNameCount'] > 0 && $taxonArr['synonymCount'] == 0){
$url = 'http://services.tropicos.org/Name/'.$id.'/AcceptedNames?apikey='.$this->taxonomicResources['tropicos'].'&format=json';
$url = 'https://services.tropicos.org/Name/'.$id.'/AcceptedNames?apikey='.$this->taxonomicResources['tropicos'].'&format=json';
if($fh = fopen($url, 'r')){
$content = '';
while($line = fread($fh, 1024)){
Expand Down Expand Up @@ -907,14 +925,18 @@ private function getTropicosNode($nodeArr){
if(isset($nodeArr['Genus'])) $taxonArr['unitname1'] = $nodeArr['Genus'];
if(isset($nodeArr['SpeciesEpithet'])) $taxonArr['unitname2'] = $nodeArr['SpeciesEpithet'];
if(isset($nodeArr['source'])) $taxonArr['source'] = $nodeArr['source'];
if(!isset($taxonArr['unitname1']) && !strpos($taxonArr['sciname'],' ')) $taxonArr['unitname1'] = $taxonArr['sciname'];
if(!isset($taxonArr['unitname1']) && $taxonArr['sciname'] && !strpos($taxonArr['sciname'],' ')) $taxonArr['unitname1'] = $taxonArr['sciname'];
$taxonArr['rankid'] = $this->getRankIdByTaxonArr($taxonArr);
if(isset($taxonArr['unitname2']) && isset($nodeArr['OtherEpithet'])){
$taxonArr['unitname3'] = $nodeArr['OtherEpithet'];
if($this->kingdomName != 'Animalia'){
if($taxonArr['rankid'] == 230) $taxonArr['unitind3'] = 'subsp.';
elseif($taxonArr['rankid'] == 240) $taxonArr['unitind3'] = 'var.';
elseif($taxonArr['rankid'] == 260) $taxonArr['unitind3'] = 'f.';
elseif($taxonArr['rankid'] == 260){
$taxonArr['unitind3'] = 'f.';
$taxonArr['sciname'] = str_replace(' fo. ', ' f. ', $taxonArr['sciname']);
}

}
}
return $taxonArr;
Expand Down Expand Up @@ -1161,7 +1183,7 @@ private function loadNewTaxon($taxonArr, $tidAccepted = 0){
$sql = 'SELECT tidaccepted FROM taxstatus WHERE (taxauthid = '.$this->taxAuthId.') AND (tid = '.$newTid.')';
$rs = $this->conn->query($sql);
if($r = $rs->fetch_object()){
//Taxon is already in this thesaurus, thus link synonyms to accepted name of this taxon
//Taxon is already in this thesaurus, thus skip loading and jsut link synonyms to accepted name of this taxon
$tidAccepted = $r->tidaccepted;
$loadTaxon= false;
}
Expand Down Expand Up @@ -1412,38 +1434,37 @@ public function getCloseMatch($taxonStr){
$retArr = array();
$taxonStr = $this->cleanInStr($taxonStr);
if($taxonStr){
$infraArr = array('subsp','ssp','var','f');
$taxonStringArr = explode(' ',$taxonStr);
$unitname1 = array_shift($taxonStringArr);
if(strlen($unitname1) == 1) $unitname1 = array_shift($taxonStringArr);
$unitname2 = array_shift($taxonStringArr);
if(strlen($unitname2) == 1) $unitname2 = array_shift($taxonStringArr);
$unitname3 = array_shift($taxonStringArr);
if($taxonStringArr){
while($val = array_shift($taxonStringArr)){
if(in_array(str_replace('.', '', $val),$infraArr)) $unitname3 = array_shift($taxonStringArr);
$infraArr = array('subsp.','ssp.','var.','f.');
$unitArr = explode(' ', $taxonStr);
$unitname1 = $this->cleanInStr(array_shift($unitArr));
if(strlen($unitname1) == 1) $unitname1 = $this->cleanInStr(array_shift($unitArr));
$unitname2 = $this->cleanInStr(array_shift($unitArr));
if(strlen($unitname2) == 1) $unitname2 = $this->cleanInStr(array_shift($unitArr));
$infraEpithetArr = array();
foreach($unitArr as $str){
if(!in_array($str, $infraArr)){
$infraEpithetArr[] = $this->cleanInStr($str);
}
}
if($unitname3){
if($infraEpithetArr){
//Look for infraspecific species with different rank indicators
$sql = 'SELECT tid, sciname FROM taxa WHERE (unitname1 = "'.$unitname1.'") AND (unitname2 = "'.$unitname2.'") AND (unitname3 = "'.$unitname3.'") ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->kingdomName.'" OR kingdomname IS NULL) ';
$sql = 'SELECT tid, sciname FROM taxa WHERE (unitname1 = "'.$unitname1.'") AND (unitname2 = "'.$unitname2.'") ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->cleanInStr($this->kingdomName).'" OR kingdomname IS NULL) ';
$sql .= 'ORDER BY sciname';
$rs = $this->conn->query($sql);
while($row = $rs->fetch_object()){
$retArr[$row->tid] = $row->sciname;
}
$rs->free();
}

if($unitname2){
if(!$retArr){
//Look for match where
$searchStr = substr($unitname1,0,4).'%';
$searchStr .= ' '.substr($unitname2,0,4).'%';
if(strlen($unitname3) > 2) $searchStr .= ' '.substr($unitname3,0,5).'%';
$searchStr = substr($unitname1, 0, 4).'%';
$searchStr .= ' '.substr($unitname2, 0, 4).'%';
if($infraEpithetArr) $searchStr .= ' '.substr($infraEpithetArr[0], 0, 5).'%';
$sql = 'SELECT tid, sciname FROM taxa WHERE (sciname LIKE "'.$searchStr.'") ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->kingdomName.'" OR kingdomname IS NULL) ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->cleanInStr($this->kingdomName).'" OR kingdomname IS NULL) ';
$sql .= 'ORDER BY sciname LIMIT 15';
$rs = $this->conn->query($sql);
while($row = $rs->fetch_object()){
Expand All @@ -1457,7 +1478,7 @@ public function getCloseMatch($taxonStr){
if(!$retArr){
//Look for matches based on same edithet but different genus
$sql = 'SELECT tid, sciname FROM taxa WHERE (sciname LIKE "'.substr($unitname1,0,2).'% '.$unitname2.'") ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->kingdomName.'" OR kingdomname IS NULL) ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->cleanInStr($this->kingdomName).'" OR kingdomname IS NULL) ';
$sql .= 'ORDER BY sciname';
$rs = $this->conn->query($sql);
while($row = $rs->fetch_object()){
Expand All @@ -1467,8 +1488,8 @@ public function getCloseMatch($taxonStr){
}
}
//Get soundex matches
$sql = 'SELECT tid, sciname FROM taxa WHERE SOUNDEX(sciname) = SOUNDEX("'.$taxonStr.'") ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->kingdomName.'" OR kingdomname IS NULL) ';
$sql = 'SELECT tid, sciname FROM taxa WHERE SOUNDEX(sciname) = SOUNDEX("'.$this->cleanInStr($taxonStr).'") ';
if($this->kingdomName) $sql .= 'AND (kingdomname = "'.$this->cleanInStr($this->kingdomName).'" OR kingdomname IS NULL) ';
$sql .= 'ORDER BY sciname LIMIT 5';
$rs = $this->conn->query($sql);
while($row = $rs->fetch_object()){
Expand Down Expand Up @@ -1742,6 +1763,7 @@ private function setRankIdArr(){
if(isset($this->rankIdArr['form'])){
$this->rankIdArr['f.'] = $this->rankIdArr['form'];
$this->rankIdArr['fo.'] = $this->rankIdArr['form'];
$this->rankIdArr['forma'] = $this->rankIdArr['form'];
}
}
}
Expand Down
2 changes: 1 addition & 1 deletion config/symbbase.php
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
header('X-Frame-Options: DENY');
header('Cache-control: private'); // IE 6 FIX
date_default_timezone_set('America/Phoenix');
$CODE_VERSION = '3.0.8';
$CODE_VERSION = '3.0.9';

if(!isset($CLIENT_ROOT) && isset($clientRoot)) $CLIENT_ROOT = $clientRoot;
if(substr($CLIENT_ROOT,-1) == '/') $CLIENT_ROOT = substr($CLIENT_ROOT,0,strlen($CLIENT_ROOT)-1);
Expand Down

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