Hotfix v.3.1.3 (#1821)

* Hotfix v3.1.3 - Adjusted hotfix merge instructions - Inventory Management: Bug fix interfering with adding new editors to an inventory project - Image migration modifications -- Add option to copy over existing target files -- Add checks and error handling for non-existent source files and already existing target files -- Direct log files to be written to /content/logs/ - fix misspelled log directory name, with support still maintained for portals that already have the misspelled directory - Fix jquery selector to be correct so button is enabled when trait is changed - Misc language file and wording adjustments
BioKIC · Nov 4, 2024 · 258f4b9 · 258f4b9
1 parent db367a2
commit 258f4b9
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Showing 28 changed files with 183 additions and 52 deletions.
diff --git a/checklists/checklist.php b/checklists/checklist.php
@@ -402,7 +402,7 @@ function changeImageSource(elem){
 											foreach($clidArr as $id){
 												?>
 												<a href="#" onclick="return openPopup('clsppeditor.php?tid=<?php echo $tid . '&clid=' . $id; ?>','editorwindow');">
-													<img src='../images/edit.png' style='width:1.3em;' alt="<?php echo $LANG['IMG_EDIT_DETAILS']; ?>" title='<?php echo $LANG['EDIT_DETAILS']; ?>' />
+													<img src='../images/edit.png' style='width:1.3em;' alt="<?php echo $LANG['EDIT_DETAILS']; ?>" title='<?php echo $LANG['EDIT_DETAILS']; ?>' />
 												</a>
 												<?php
 											}

diff --git a/classes/MediaResolutionTools.php b/classes/MediaResolutionTools.php
@@ -11,6 +11,7 @@ class MediaResolutionTools extends Manager {
 	private $deleteOriginal = false;
 
 	//Image migration variables
+	private $collid;
 	private $collMetaArr;
 	private $transferThumbnail = false;
 	private $transferWeb = false;
@@ -23,14 +24,12 @@ class MediaResolutionTools extends Manager {
 	private $imgRootPath;
 	private $imgSubPath;
 	private $sourcePathPrefix;
+	private $copyOverExistingImages = false;
 
 	private $debugMode = false;
 
 	function __construct() {
 		parent::__construct(null,'write');
-		set_time_limit(600);
-		$this->verboseMode = 3;
-		$this->setLogFH('../../../temp/logs/imgMigration_'.date('Ym').'.log');
 	}
 
 	function __destruct(){
@@ -39,7 +38,12 @@ function __destruct(){
 
 	//Archiver functions
 	public function archiveImageFiles($imgidStart, $limit){
-		//Set stage
+		set_time_limit(1200);
+		$this->verboseMode = 3;
+		$logPath = $GLOBALS['SERVER_ROOT'] . '/content/logs/imageprocessing/';
+		if(!file_exists($logPath)) mkdir($logPath);
+		$logPath .= 'imgArchive_' . date('Ym') . '.log';
+		$this->setLogFH($logPath);
 		if(!$imgidStart) $imgidStart = 0;
 		if(!$this->imgidArr){
 			$this->logOrEcho('ABORTED: Image ids (imgid) not supplied');
@@ -165,8 +169,13 @@ private function archiveImage($imgFilePath, $imgid){
 
 	//Image migration functions
 	public function migrateFieldDerivatives($imgIdStart, $limit){
+		set_time_limit(1200);
+		$this->verboseMode = 3;
+		$logPath = $GLOBALS['SERVER_ROOT'] . '/content/logs/imageprocessing/';
+		if(!file_exists($logPath)) mkdir($logPath);
+		$logPath .= 'fieldDerivativeMigration_' . date('Ym') . '.log';
+		$this->setLogFH($logPath);
 		//Needs to be reworked
-		ini_set('max_execution_time', 3600);
 		$this->debugMode = true;
 		$imgId = 0;
 		if(is_numeric($limit) && is_numeric($this->collid) && $this->imgRootUrl && $this->imgRootPath){
@@ -249,7 +258,12 @@ public function migrateFieldDerivatives($imgIdStart, $limit){
 
 	public function migrateCollectionDerivatives($imgIdStart, $limit){
 		//Migrates images based on catalog number; NULL or weak catalogNumbers are skipped
-		ini_set('max_execution_time', 3600);
+		set_time_limit(1200);
+		$this->verboseMode = 3;
+		$logPath = $GLOBALS['SERVER_ROOT'] . '/content/logs/imageprocessing/';
+		if(!file_exists($logPath)) mkdir($logPath);
+		$logPath .= 'imgMigration_' . date('Ym') . '.log';
+		$this->setLogFH($logPath);
 		if($this->collid && is_numeric($limit) && $this->imgRootUrl && $this->imgRootPath){
 			if($this->transferThumbnail || $this->transferWeb || $this->transferLarge){
 				if($this->matchTermThumbnail || $this->matchTermWeb || $this->matchTermLarge){
@@ -294,53 +308,83 @@ public function migrateCollectionDerivatives($imgIdStart, $limit){
 								$targetPath = $this->imgRootPath.$pathFrag.$fileName;
 								$targetUrl = $this->imgRootUrl.$pathFrag.$fileName;
 								$thumbPath = $this->getLocalPath($r->thumbnailurl);
-								if(copy($thumbPath, $targetPath)){
-									$imgArr[$r->imgid]['tn'] = $targetUrl;
-									$this->logOrEcho('Copied: '.$thumbPath.' => '.$targetPath,1);
-									if($this->deleteSource){
-										if(unlink($thumbPath)){
-											$this->logOrEcho('Source deleted: '.$thumbPath,1);
-										}
-										else{
-											$this->logOrEcho('ERROR deleting source (file permissions?): '.$thumbPath,1);
+								if(file_exists($thumbPath)){
+									if($this->copyOverExistingImages || !file_exists($targetPath)){
+										if(copy($thumbPath, $targetPath)){
+											$imgArr[$r->imgid]['tn'] = $targetUrl;
+											$this->logOrEcho('Copied: '.$thumbPath.' => '.$targetPath,1);
+											if($this->deleteSource){
+												if(unlink($thumbPath)){
+													$this->logOrEcho('Source deleted: '.$thumbPath,1);
+												}
+												else{
+													$this->logOrEcho('ERROR deleting source (file permissions?): '.$thumbPath,1);
+												}
+											}
 										}
 									}
+									else{
+										$this->logOrEcho('Skipped: target file already exists (' . $targetPath . ')', 1);
+									}
+								}
+								else{
+									$this->logOrEcho('Skipped: source thumbnail does not exist (' . $thumbPath . ')', 1);
 								}
 							}
 							if($this->transferWeb && $r->url){
 								$fileName = basename($r->url);
 								$targetPath = $this->imgRootPath.$pathFrag.$fileName;
 								$targetUrl = $this->imgRootUrl.$pathFrag.$fileName;
 								$urlPath = $this->getLocalPath($r->url);
-								if(copy($urlPath, $targetPath)){
-									$imgArr[$r->imgid]['web'] = $targetUrl;
-									$this->logOrEcho('Copied: '.$urlPath.' => '.$targetPath,1);
-									if($this->deleteSource){
-										if(unlink($urlPath)){
-											$this->logOrEcho('Source delete: '.$urlPath,1);
-										}
-										else{
-											$this->logOrEcho('ERROR deleting source (file permissions?): '.$urlPath,1);
+								if(file_exists($urlPath)){
+									if($this->copyOverExistingImages || !file_exists($targetPath)){
+										if(copy($urlPath, $targetPath)){
+											$imgArr[$r->imgid]['web'] = $targetUrl;
+											$this->logOrEcho('Copied: '.$urlPath.' => '.$targetPath,1);
+											if($this->deleteSource){
+												if(unlink($urlPath)){
+													$this->logOrEcho('Source delete: '.$urlPath,1);
+												}
+												else{
+													$this->logOrEcho('ERROR deleting source (file permissions?): '.$urlPath,1);
+												}
+											}
 										}
 									}
+									else{
+										$this->logOrEcho('Skipped: target file already exists (' . $targetPath . ')', 1);
+									}
+								}
+								else{
+									$this->logOrEcho('Skipped: source file does not exist (' . $urlPath . ')', 1);
 								}
 							}
 							if($this->transferLarge && $r->originalurl){
 								$fileName = basename($r->originalurl);
 								$targetPath = $this->imgRootPath.$pathFrag.$fileName;
 								$targetUrl = $this->imgRootUrl.$pathFrag.$fileName;
 								$origPath = $this->getLocalPath($r->originalurl);
-								if(copy($origPath, $targetPath)){
-									$imgArr[$r->imgid]['lg'] = $targetUrl;
-									$this->logOrEcho('Copied: '.$origPath.' => '.$targetPath,1);
-									if($this->deleteSource){
-										if(unlink($origPath)){
-											$this->logOrEcho('Source deleted: '.$origPath,1);
-										}
-										else{
-											$this->logOrEcho('ERROR deleting source (file permissions?): '.$origPath,1);
+								if(file_exists($origPath)){
+									if($this->copyOverExistingImages || !file_exists($targetPath)){
+										if(copy($origPath, $targetPath)){
+											$imgArr[$r->imgid]['lg'] = $targetUrl;
+											$this->logOrEcho('Copied: '.$origPath.' => '.$targetPath,1);
+											if($this->deleteSource){
+												if(unlink($origPath)){
+													$this->logOrEcho('Source deleted: '.$origPath,1);
+												}
+												else{
+													$this->logOrEcho('ERROR deleting source (file permissions?): '.$origPath,1);
+												}
+											}
 										}
 									}
+									else{
+										$this->logOrEcho('Skipped: target file already exists (' . $targetPath . ')', 1);
+									}
+								}
+								else{
+									$this->logOrEcho('Skipped: source file does not exist (' . $origPath . ')', 1);
 								}
 							}
 							$processingCnt++;
@@ -567,5 +611,10 @@ public function setImgRootPath($url){
 	public function setImgSubPath($path){
 		$this->imgSubPath = $path;
 	}
+
+	public function setCopyOverExistingImages($bool){
+		if($bool) $this->copyOverExistingImages = true;
+		else $this->copyOverExistingImages = false;
+	}
 }
 ?>
diff --git a/classes/SpecProcessorManager.php b/classes/SpecProcessorManager.php
@@ -579,7 +579,7 @@ public function downloadReportData($target){
 	public function getLogListing(){
 		$retArr = array();
 		if($this->collid){
-			$dirArr = array('imgProccessing','cyverse','iplant','processing/imgmap');
+			$dirArr = array('imageprocessing','imgProccessing','cyverse','iplant','processing/imgmap');
 			foreach($dirArr as $dirPath){
 				if(file_exists($this->logPath.$dirPath)){
 					if($fh = opendir($this->logPath.$dirPath)){

diff --git a/collections/admin/importextended.php b/collections/admin/importextended.php
@@ -194,7 +194,7 @@ function importTypeChanged(selectElement){
 				<?= $LANG['INSTRUCTIONS'] ?>:
 				<ul>
 					<li><a href="https://biokic.github.io/symbiota-docs/coll_manager/upload/links" target="_blank"><?= $LANG['ASSOCIATIONS'] ?></a></li>
-					<?php if($IS_ADMIN) echo '<li><a href="https://biokic.github.io/symbiota-docs/coll_manager/upload/determinations" target="_blank">'.$LANG['DETERMINATIONS'].'</a></li>'; ?>
+					<?php if($IS_ADMIN) echo '<li><a href="https://biokic.github.io/symbiota-docs/portal_manager/determinations" target="_blank">'.$LANG['DETERMINATIONS'].'</a></li>'; ?>
 					<li><a href="https://biokic.github.io/symbiota-docs/coll_manager/images/url_upload" target="_blank"><?= $LANG['IMAGE_URLS'] ?></a></li>
 				</ul>
 			</div>

diff --git a/collections/map/index.php b/collections/map/index.php
@@ -423,7 +423,7 @@ function buildTaxaLegend() {
 					taxaHtml += "<div style='display:table;'>";
 					prev_family = taxa.family;
 				}
-				const sn_link = `<a target="_blank" href="${taxa.origin}/taxa/index.php?tid=${taxa.tid}">${taxa.sn}</a>`;
+				const sn_link = `<a target="_blank" href="${taxa.origin? taxa.origin: '<?= $CLIENT_ROOT ?>'}/taxa/index.php?tid=${taxa.tid}">${taxa.sn}</a>`;
 				taxaHtml += legendRow(`taxa-${taxa.id_map.map(id => `${id.index}*${id.tid}`).join(",")}`, taxa.color, sn_link);
 			}
 

diff --git a/collections/map/rpc/searchCollections.php b/collections/map/rpc/searchCollections.php
@@ -50,7 +50,7 @@
 
 $host = false;
 if(isset($SERVER_HOST)) {
-   $host = (str_contains($SERVER_HOST, '127.0.0.1') || str_contains($SERVER_HOST, 'localhost')? "http://": "https://") . $SERVER_HOST . $CLIENT_ROOT;
+   $host = ((str_contains($SERVER_HOST, '127.0.0.1') || str_contains($SERVER_HOST, 'localhost'))? "http://": "https://") . $SERVER_HOST . $CLIENT_ROOT;
 }
 
 foreach ($coordArr as $collName => $coll) {

diff --git a/collections/search/index.php b/collections/search/index.php
@@ -416,7 +416,7 @@
 										<input type="text" name="catnum" id="catnum" data-chip="<?php echo $LANG['CATALOG_NUMBER'] ?>" />
 										<span class="inset-input-label"><?php echo $LANG['CATALOG_NUMBER'] ?></span>
 									</label>
-									<span class="assistive-text"><?php echo $LANG['SEPARATE_MULTIPLE_W_COMMA'] ?></span>
+									<span class="assistive-text"><?php echo $LANG['SEPARATE_MULTIPLE_W_COMMA_DASH'] ?></span>
 								</div>
 							</div>
 							<div>

diff --git a/collections/specprocessor/imageprocessor.php b/collections/specprocessor/imageprocessor.php
@@ -738,7 +738,8 @@ function validateFileUploadForm(f){
 							$logPath = '../../content/logs/';
 							foreach($logArr as $logCat => $logList){
 								echo '<div style="font-weight:bold;margin: 10px 0px 5px 0px">';
-								if($logCat=='imgProccessing') echo $LANG['GEN_PROCESSING'];
+								if($logCat=='imageprocessing') echo $LANG['GEN_PROCESSING'];
+								elseif($logCat=='imgProccessing') echo $LANG['GEN_PROCESSING'];
 								elseif($logCat=='iplant') echo $LANG['IPLANT'];
 								elseif($logCat=='cyverse') echo $LANG['CYVERSE'];
 								elseif($logCat=='processing/imgmap') echo $LANG['IMG_MAP_FILE'];

diff --git a/collections/specprocessor/processor.php b/collections/specprocessor/processor.php
@@ -76,7 +76,7 @@
 						$imageProcessor = new ImageLocalProcessor();
 
 						$imageProcessor->setLogMode(3);
-						$logPath = $SERVER_ROOT.(substr($SERVER_ROOT,-1) == '/'?'':'/').'content/logs/imgProccessing';
+						$logPath = $SERVER_ROOT . (substr($SERVER_ROOT, -1) == '/' ? '' : '/') . 'content/logs/imageprocessing';
 						if(!file_exists($logPath)) mkdir($logPath);
 						$imageProcessor->setLogPath($logPath);
 						$logFile = $collid.'_'.$specManager->getInstitutionCode();

diff --git a/collections/specprocessor/standalone_scripts/media_scripts.php b/collections/specprocessor/standalone_scripts/media_scripts.php
@@ -27,6 +27,7 @@
 $imgRootUrl = (array_key_exists('imgRootUrl', $_POST)?$_POST['imgRootUrl']:'');
 $imgRootPath = (array_key_exists('imgRootPath', $_POST)?$_POST['imgRootPath']:'');
 $imgSubPath = (array_key_exists('imgSubPath', $_POST)?$_POST['imgSubPath']:'');
+$copyover = (!empty($_POST['copyover']) ? 1 : 0);
 $submit = (array_key_exists('submitbutton', $_POST)?$_POST['submitbutton']:'');
 
 //Sanitation
@@ -107,6 +108,7 @@ function verifyMigrationCode(f){
 							$toolManager->setImgRootUrl($imgRootUrl);
 							$toolManager->setImgRootPath($imgRootPath);
 							$toolManager->setImgSubPath($imgSubPath);
+							$toolManager->setCopyOverExistingImages($copyover);
 							if($collid) $imgIdStart = $toolManager->migrateCollectionDerivatives($imgIdStart, $limit);
 							else $imgIdStart = $toolManager->migrateFieldDerivatives($imgIdStart, $limit);
 							?>
@@ -287,6 +289,12 @@ function verifyMigrationCode(f){
 							</div>
 						</fieldset>
 					</div>
+					<div class="fieldRowDiv">
+						<div class="fieldDiv">
+							<input type="checkbox" name="copyover" value="1" <?= ($copyover ? 'checked' : '') ?>>
+							<span class="fieldLabel">copyover existing target images</span>
+						</div>
+					</div>
 					<div class="fieldRowDiv">
 						<div class="fieldDiv">
 							<span class="fieldLabel">imgId start:</span>

diff --git a/config/symbbase.php b/config/symbbase.php
@@ -2,7 +2,7 @@
 header('X-Frame-Options: DENY');
 header('Cache-control: private'); // IE 6 FIX
 date_default_timezone_set('America/Phoenix');
-$CODE_VERSION = '3.1.2';
+$CODE_VERSION = '3.1.3';
 
 set_include_path(get_include_path() . PATH_SEPARATOR . $SERVER_ROOT . PATH_SEPARATOR . $SERVER_ROOT.'/config/' . PATH_SEPARATOR . $SERVER_ROOT.'/classes/');
 

diff --git a/content/lang/collections/map/index.en.php b/content/lang/collections/map/index.en.php
@@ -14,6 +14,7 @@
 $LANG['RESET'] = 'Reset';
 $LANG['SEARCH'] = 'Search';
 $LANG['TAXA'] = 'Taxa';
+$LANG['WITHIN'] = 'within';
 $LANG['SHAPE_TOOLS'] = 'Use the shape tools on the map to select occurrences within a given shape';
 $LANG['WITHIN_POLYGON'] = 'Within the selected polygon';
 $LANG['WITHIN_CIRCLE'] = 'Within the selected circle';

diff --git a/content/lang/collections/map/index.es.php b/content/lang/collections/map/index.es.php
@@ -3,7 +3,9 @@
 ------------------
 Language: Español (Spanish)
 Translated by: Samanta Orellana
+Edited by: Katie Pearson
 Date Translated: 2021-06-23
+Date Edited: 2024-10-22
 ------------------
 */
 include_once($SERVER_ROOT.'/content/lang/collections/harvestparams.es.php');
@@ -16,6 +18,7 @@
 $LANG['RESET'] = 'Reiniciar';
 $LANG['SEARCH'] = 'Buscar';
 $LANG['TAXA'] = 'Taxa';
+$LANG['WITHIN'] = ''; //empty because correct phrasing is "a _ de mí"
 $LANG['SHAPE_TOOLS'] = 'Use las herramientas de formas sobre el mapa para seleccionar los registros dentro de dicha forma';
 $LANG['WITHIN_POLYGON'] = 'Dentro del polígono seleccionado';
 $LANG['WITHIN_CIRCLE'] = 'Dentro del círculo seleccionado';

diff --git a/content/lang/collections/map/index.fr.php b/content/lang/collections/map/index.fr.php
@@ -14,6 +14,7 @@
 $LANG['RESET'] = 'Réinitialiser';
 $LANG['SEARCH'] = 'Recherche';
 $LANG['TAXA'] = 'Taxa';
+$LANG['WITHIN'] = 'à moins de';
 $LANG['SHAPE_TOOLS'] = 'Utilisez les outils de forme sur la carte pour sélectionner des occurrences dans une forme donnée';
 $LANG['WITHIN_POLYGON'] = 'Dans le polygone sélectionné';
 $LANG['WITHIN_CIRCLE'] = 'Dans le cercle sélectionné';

diff --git a/content/lang/collections/map/index.pt.php b/content/lang/collections/map/index.pt.php
@@ -7,6 +7,7 @@
 ------------------
 */
 include_once($SERVER_ROOT.'/content/lang/collections/harvestparams.pt.php');
+include_once('mapshared.pt.php');
 
 $LANG['SEARCH_CRITERIA'] = 'Critérios de Pesquisa';
 $LANG['CRITERIA'] = 'Critérios';
@@ -15,6 +16,7 @@
 $LANG['RESET'] = 'Redefinir';
 $LANG['SEARCH'] = 'Pesquisar';
 $LANG['TAXA'] = 'Taxa';
+$LANG['WITHIN'] = ''; //empty because correct phrasing is "a _ de mim"
 $LANG['SHAPE_TOOLS'] = 'Use as ferramentas de forma no mapa para selecionar ocorrências dentro de uma determinada forma';
 $LANG['WITHIN_POLYGON'] = 'Dentro do polígono selecionado';
 $LANG['WITHIN_CIRCLE'] = 'Dentro do círculo selecionado';

diff --git a/content/lang/collections/map/mapshared.pt.php b/content/lang/collections/map/mapshared.pt.php
@@ -0,0 +1,17 @@
+<?php
+/*
+------------------
+Language: Português (Portuguese)
+Translated by: Google Translate
+Date Translated: 2024-10-22
+------------------
+*/
+$LANG['LATITUDE'] = 'Latitude';
+$LANG['LONGITUDE'] = 'Longitude';
+
+$LANG['COLLECTION'] = 'Coleção';
+$LANG['OBSERVATION'] = 'Observação';
+
+$LANG['DECIMAL'] = 'Decimal';
+$LANG['DEGREE'] = 'Grau';
+?>
diff --git a/content/lang/collections/search/index.en.php b/content/lang/collections/search/index.en.php
@@ -22,6 +22,7 @@
 $LANG['INCLUDE_CATA_NUM_GUIDs'] = 'Include other catalog numbers and GUIDs';
 $LANG['CATALOG_NUMBER'] = 'Catalog Number';
 $LANG['SEPARATE_MULTIPLE_W_COMMA'] = 'Separate multiple with commas.';
+$LANG['SEPARATE_MULTIPLE_W_COMMA_DASH'] = 'Separate multiple with commas or provide ranges with a dash.';
 $LANG['LIMIT_TO_SPECIMENS_W_IMAGES'] = 'Limit to specimens with images';
 $LANG['LIMIT_TO_SPECIMENS_W_GENETIC_DATA'] = 'Limit to specimens with genetic data';
 $LANG['LOCALITY'] = 'Locality';
@@ -87,7 +88,7 @@
 $LANG['ONLY_WITH_IMAGES'] = 'Only with images';
 $LANG['ONLY_WITH_GENETIC'] = 'Only with genetic';
 $LANG['ONLY_WITH_COORDINATES'] = 'Only with coordinates';
-$LANG['INCLUDE_CULTIVATED'] = 'Include cultivated';
+$LANG['INCLUDE_CULTIVATED'] = 'Include cultivated/captive';
 $LANG['MIN_ELEVATION'] = 'Min Elevation';
 $LANG['MAX_ELEVATION'] = 'Max Elevation';
 $LANG['UPPER_LAT'] = 'Upper Lat';

diff --git a/content/lang/collections/search/index.es.php b/content/lang/collections/search/index.es.php
@@ -24,6 +24,7 @@
 $LANG['INCLUDE_CATA_NUM_GUIDs'] = 'Incluir otros números de catálogo y GUID';
 $LANG['CATALOG_NUMBER'] = 'Número de catálogo';
 $LANG['SEPARATE_MULTIPLE_W_COMMA'] = 'Separar varios con comas.';
+$LANG['SEPARATE_MULTIPLE_W_COMMA_DASH'] = 'Separe números múltiples con comas o proporcione rangos con un guión.';
 $LANG['LIMIT_TO_SPECIMENS_W_IMAGES'] = 'Limitar a especímenes con imágenes';
 $LANG['LIMIT_TO_SPECIMENS_W_GENETIC_DATA'] = 'Limitar a especímenes con datos genéticos';
 $LANG['LOCALITY'] = 'Localidad';