[3.3] 1924 export associations as resource relationship

.vscode/launch.json

@@ -1,48 +1,51 @@
 {
-    // Use IntelliSense to learn about possible attributes.
-    // Hover to view descriptions of existing attributes.
-    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
-    "version": "0.2.0",
-    "configurations": [
-        {
-            "name": "Listen for Xdebug",
-            "type": "php",
-            "request": "launch",
-            "port": 9003
-        },
-        {
-            "name": "Launch currently open script",
-            "type": "php",
-            "request": "launch",
-            "program": "${file}",
-            "cwd": "${fileDirname}",
-            "port": 0,
-            "runtimeArgs": [
-                "-dxdebug.start_with_request=yes"
-            ],
-            "env": {
-                "XDEBUG_MODE": "debug,develop",
-                "XDEBUG_CONFIG": "client_port=${port}"
-            }
-        },
-        {
-            "name": "Launch Built-in web server",
-            "type": "php",
-            "request": "launch",
-            "runtimeArgs": [
-                "-dxdebug.mode=debug",
-                "-dxdebug.start_with_request=yes",
-                "-S",
-                "localhost:0"
-            ],
-            "program": "",
-            "cwd": "${workspaceRoot}",
-            "port": 9003,
-            "serverReadyAction": {
-                "pattern": "Development Server \\(http://localhost:([0-9]+)\\) started",
-                "uriFormat": "http://localhost:%s",
-                "action": "openExternally"
-            }
-        }
-    ]
-}
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Listen for Xdebug",
+      "type": "php",
+      "request": "launch",
+      "port": 9003,
+      "xdebugSettings": {
+        "max_children": 128,
+        "max_data": -1,
+        "max_depth": 3
+      }
+    },
+    {
+      "name": "Launch currently open script",
+      "type": "php",
+      "request": "launch",
+      "program": "${file}",
+      "cwd": "${fileDirname}",
+      "port": 0,
+      "runtimeArgs": ["-dxdebug.start_with_request=yes"],
+      "env": {
+        "XDEBUG_MODE": "debug,develop",
+        "XDEBUG_CONFIG": "client_port=${port}"
+      }
+    },
+    {
+      "name": "Launch Built-in web server",
+      "type": "php",
+      "request": "launch",
+      "runtimeArgs": [
+        "-dxdebug.mode=debug",
+        "-dxdebug.start_with_request=yes",
+        "-S",
+        "localhost:0"
+      ],
+      "program": "",
+      "cwd": "${workspaceRoot}",
+      "port": 9003,
+      "serverReadyAction": {
+        "pattern": "Development Server \\(http://localhost:([0-9]+)\\) started",
+        "uriFormat": "http://localhost:%s",
+        "action": "openExternally"
+      }
+    }
+  ]
+}

classes/AssociationManager.php

@@ -50,32 +50,41 @@ public function getRelationshipTypes(){
 
 
 
-	public function getAssociatedRecords($associationArr) {
+	public function getAssociatedRecords($associationArr, $relationshipAccessor='relationship') {
     $sql = '';
 
-    if (array_key_exists('relationship', $associationArr) && $associationArr['relationship'] !== 'none') {
+
+
+    if (array_key_exists($relationshipAccessor, $associationArr) && $associationArr[$relationshipAccessor] !== 'none') {
         $familyJoinStr = '';
         // $shouldUseFamily = array_key_exists('associated-taxa', $associationArr) && $associationArr['associated-taxa'] == '3';
 		$shouldUseFamily = true; // fixes bug that occurs when user selects "Scientific name" taxon type instead of family and then searches for a family. Silly user.
         if ($shouldUseFamily) $familyJoinStr = 'LEFT JOIN taxstatus ts ON o.tidinterpreted = ts.tid';
 
         // "Forward" association
-        $relationshipType = (array_key_exists('relationship', $associationArr) && $associationArr['relationship'] !== 'any') ? $associationArr['relationship'] : 'IS NOT NULL';
-        $relationshipStr = (array_key_exists('relationship', $associationArr) && $associationArr['relationship'] !== 'any') ? ("='" . $relationshipType . "'") : ' IS NOT NULL';
+        $relationshipType = (array_key_exists($relationshipAccessor, $associationArr) && $associationArr[$relationshipAccessor] !== 'any') ? $associationArr[$relationshipAccessor] : 'IS NOT NULL';
+        $relationshipStr = (array_key_exists($relationshipAccessor, $associationArr) && $associationArr[$relationshipAccessor] !== 'any') ? ("='" . $relationshipType . "'") : ' IS NOT NULL';
 
 		$forwardSql = "SELECT oa.occid FROM omoccurrences o INNER JOIN omoccurassociations oa ON o.occid = oa.occidAssociate  LEFT JOIN omoccurdeterminations od ON oa.occid = od.occid " . $familyJoinStr . " WHERE oa.relationship " . $relationshipStr . " ";
 		$forwardSql .= $this->getAssociatedTaxonWhereFrag($associationArr);
 
         // "Reverse" association
-        $reverseAssociationType = (array_key_exists('relationship', $associationArr) && $associationArr['relationship'] !== 'any') ? $this->getInverseRelationshipOf($relationshipType) : 'IS NOT NULL';
-        $reverseRelationshipStr = (array_key_exists('relationship', $associationArr) && $associationArr['relationship'] !== 'any') ? ("='" . $reverseAssociationType . "'") : ' IS NOT NULL';
+        $reverseAssociationType = (array_key_exists($relationshipAccessor, $associationArr) && $associationArr[$relationshipAccessor] !== 'any') ? $this->getInverseRelationshipOf($relationshipType) : 'IS NOT NULL';
+        $reverseRelationshipStr = (array_key_exists($relationshipAccessor, $associationArr) && $associationArr[$relationshipAccessor] !== 'any') ? ("='" . $reverseAssociationType . "'") : ' IS NOT NULL';
 
 
 		$reverseSql = "SELECT oa.occidAssociate FROM omoccurrences o INNER JOIN omoccurassociations oa ON o.occid = oa.occid LEFT JOIN omoccurdeterminations od ON oa.occid = od.occid " . $familyJoinStr . " WHERE oa.relationship " . $reverseRelationshipStr . " ";
 
         $reverseSql .= $this->getAssociatedTaxonWhereFrag($associationArr);
 
-        $sql .= "AND (o.occid IN (SELECT occid FROM ( " . $forwardSql . " UNION " . $reverseSql . " ) AS occids)";
+		// External associations
+		// $externalAndObservationalSql = "SELECT oa.occid FROM omoccurrences o INNER JOIN omoccurassociations oa ON o.occid = oa.occid  LEFT JOIN omoccurdeterminations od ON oa.occid = od.occid " . $familyJoinStr . " WHERE (oa.associationType='observational' OR oa.associationType='externalOccurrence') AND oa.relationship " . $relationshipStr . " ";
+		$externalAndObservationalSql = "SELECT oa.occid FROM omoccurrences o INNER JOIN omoccurassociations oa ON o.occid = oa.occid  LEFT JOIN omoccurdeterminations od ON oa.occid = od.occid " . $familyJoinStr . " WHERE (oa.associationType='observational' OR oa.associationType='externalOccurrence') AND oa.relationship " . $relationshipStr . " ";
+		$externalAndObservationalSql .= $this->getAssociatedTaxonWhereFrag($associationArr);
+
+		// $sql .= "AND (o.occid IN (SELECT occid FROM ( " . $forwardSql . " UNION " . $reverseSql . " ) AS occids)";
+
+        $sql .= "AND (o.occid IN (SELECT occid FROM ( " . $forwardSql . " UNION " . $reverseSql . " UNION " . $externalAndObservationalSql . " ) AS occids)";
     }
     return $sql;
 }

classes/DwcArchiverBaseManager.php

@@ -32,9 +32,9 @@ protected function setFileHandler($filePath){
 		$this->writeOutRecord(array_keys($this->fieldArr['fields']));
 	}
 
-	public function writeOutRecordBlock($occidArr){
+	public function writeOutRecordBlock($occidArr, $targetField='occid'){
 		if($occidArr){
-			$sql = $this->sqlBase.' WHERE occid IN('.implode(',',$occidArr).') ';
+			$sql = $this->sqlBase.' WHERE ' . $targetField . ' IN('.implode(',',$occidArr).') ';
 			if($rs = $this->conn->query($sql)){
 				while($r = $rs->fetch_assoc()){
 					$this->encodeArr($r);

classes/DwcArchiverCore.php

@@ -6,6 +6,7 @@
 include_once($SERVER_ROOT . '/classes/DwcArchiverAttribute.php');
 include_once($SERVER_ROOT . '/classes/DwcArchiverMaterialSample.php');
 include_once($SERVER_ROOT . '/classes/DwcArchiverIdentifier.php');
+include_once($SERVER_ROOT . '/classes/DwcArchiverResourceRelationship.php');
 include_once($SERVER_ROOT . '/classes/OccurrenceTaxaManager.php');
 include_once($SERVER_ROOT . '/classes/OccurrenceAccessStats.php');
 include_once($SERVER_ROOT . '/classes/PortalIndex.php');
@@ -46,6 +47,7 @@ class DwcArchiverCore extends Manager{
 	protected $includeAttributes = 0;
 	protected $includeMaterialSample = 0;
 	protected $includeIdentifiers = 0;
+	protected $includeAssociations = 0;
 	private $hasPaleo = false;
 	private $redactLocalities = 1;
 	private $rareReaderArr = array();
@@ -55,6 +57,7 @@ class DwcArchiverCore extends Manager{
 	private $attributeHandler = null;
 	private $materialSampleHandler = null;
 	private $identierHandler = null;
+	private $associationHandler = null;
 
 	private $geolocateVariables = array();
 
@@ -875,6 +878,10 @@ public function createDwcArchive($fileNameSeed = ''){
 				$zipArchive->addFile($this->targetPath . $this->ts . '-ident' . $this->fileExt);
 				$zipArchive->renameName($this->targetPath . $this->ts . '-ident' . $this->fileExt, 'identifiers' . $this->fileExt);
 			}
+			if ($this->includeAssociations && file_exists($this->targetPath . $this->ts . '-assoc' . $this->fileExt)) {
+				$zipArchive->addFile($this->targetPath . $this->ts . '-assoc' . $this->fileExt);
+				$zipArchive->renameName($this->targetPath . $this->ts . '-assoc' . $this->fileExt, 'associations' . $this->fileExt);
+			}
 			//Meta file
 			$this->writeMetaFile();
 			$zipArchive->addFile($this->targetPath . $this->ts . '-meta.xml');
@@ -895,6 +902,7 @@ public function createDwcArchive($fileNameSeed = ''){
 			if ($this->includeAttributes && file_exists($this->targetPath . $this->ts . '-attr' . $this->fileExt)) unlink($this->targetPath . $this->ts . '-attr' . $this->fileExt);
 			if ($this->includeMaterialSample && file_exists($this->targetPath . $this->ts . '-matSample' . $this->fileExt)) unlink($this->targetPath . $this->ts . '-matSample' . $this->fileExt);
 			if ($this->includeIdentifiers && file_exists($this->targetPath . $this->ts . '-ident' . $this->fileExt)) unlink($this->targetPath . $this->ts . '-ident' . $this->fileExt);
+			if ($this->includeAssociations && file_exists($this->targetPath . $this->ts . '-assoc' . $this->fileExt)) unlink($this->targetPath . $this->ts . '-assoc' . $this->fileExt);
 			unlink($this->targetPath . $this->ts . '-meta.xml');
 			if ($this->schemaType == 'dwc') rename($this->targetPath . $this->ts . '-eml.xml', $this->targetPath . str_replace('.zip', '.eml', $fileName));
 			else unlink($this->targetPath . $this->ts . '-eml.xml');
@@ -1120,6 +1128,35 @@ private function writeMetaFile(){
 			$rootElem->appendChild($extElem3);
 		}
 
+		//Association/Resource relationship extension  https://rs.gbif.org/extension/resource_relationship_2024-02-19.xml
+		if ($this->includeAssociations && isset($this->fieldArrMap['associations'])) {
+			$extElem3 = $newDoc->createElement('extension');
+			$extElem3->setAttribute('encoding', $this->charSetOut);
+			$extElem3->setAttribute('fieldsTerminatedBy', $this->delimiter);
+			$extElem3->setAttribute('linesTerminatedBy', '\n');
+			$extElem3->setAttribute('fieldsEnclosedBy', '"');
+			$extElem3->setAttribute('ignoreHeaderLines', '1');
+			$extElem3->setAttribute('rowType', 'http://rs.tdwg.org/dwc/terms/ResourceRelationship');
+
+			$filesElem3 = $newDoc->createElement('files');
+			$filesElem3->appendChild($newDoc->createElement('location', 'associations' . $this->fileExt));
+			$extElem3->appendChild($filesElem3);
+
+			$coreIdElem3 = $newDoc->createElement('coreid');
+			$coreIdElem3->setAttribute('index', '0');
+			$extElem3->appendChild($coreIdElem3);
+
+			$mofCnt = 1;
+			foreach ($this->fieldArrMap['associations'] as $term) {
+				$fieldElem = $newDoc->createElement('field');
+				$fieldElem->setAttribute('index', $mofCnt);
+				$fieldElem->setAttribute('term', $term);
+				$extElem3->appendChild($fieldElem);
+				$mofCnt++;
+			}
+			$rootElem->appendChild($extElem3);
+		}
+
 		$newDoc->save($this->targetPath . $this->ts . '-meta.xml');
 
 		$this->logOrEcho('Done! (' . date('h:i:s A') . ")\n", 1);
@@ -1801,9 +1838,9 @@ private function writeOccurrenceFile(){
 						//$dynProp = $r['dynamicProperties'] . '; ' . $dynProp;
 						//$r['dynamicProperties'] = $dynProp;
 					}
-					if ($assocOccurStr = $dwcOccurManager->getAssociationStr($r['occid'])) $r['t_associatedOccurrences'] = $assocOccurStr;
+					// if ($assocOccurStr = $dwcOccurManager->getAssociationStr($r['occid'])) $r['t_associatedOccurrences'] = $assocOccurStr;
 					if ($assocSeqStr = $dwcOccurManager->getAssociatedSequencesStr($r['occid'])) $r['t_associatedSequences'] = $assocSeqStr;
-					if ($assocTaxa = $dwcOccurManager->getAssociationStr($r['occid'], 'observational')) $r['associatedTaxa'] = $assocTaxa;
+					// if ($assocTaxa = $dwcOccurManager->getAssociationStr($r['occid'], 'observational')) $r['associatedTaxa'] = $assocTaxa;
 				}
 				//$dwcOccurManager->appendUpperTaxonomy($r);
 				$dwcOccurManager->appendUpperTaxonomy2($r);
@@ -1822,6 +1859,7 @@ private function writeOccurrenceFile(){
 					if ($this->includeAttributes) $this->writeAttributeData($batchOccidArr);
 					if ($this->includeMaterialSample) $this->writeMaterialSampleData($batchOccidArr);
 					if ($this->includeIdentifiers) $this->writeIdentifierData($batchOccidArr);
+					if ($this->includeAssociations) $this->writeAssociationData($batchOccidArr);
 					if ($pubID && $portalManager) $portalManager->insertPortalOccurrences($pubID, $batchOccidArr);
 					unset($batchOccidArr);
 					$batchOccidArr = array();
@@ -1850,6 +1888,10 @@ private function writeOccurrenceFile(){
 				$this->writeIdentifierData($batchOccidArr);
 				$this->identierHandler = null;
 			}
+			if ($this->includeAssociations){
+				$this->writeAssociationData($batchOccidArr);
+				$this->associationHandler = null;
+			}
 		}
 		else {
 			$this->errorMessage = 'ERROR creating occurrence file: ' . $this->conn->error;
@@ -1868,6 +1910,7 @@ private function writeOccurrenceFile(){
 		if ($this->includeAttributes) $this->logOrEcho('Occurrence Attributes exported as a MeasurementsOrFact extension file... ');
 		if ($this->includeMaterialSample) $this->logOrEcho('Material Samples exported within a MaterialSample extension file... ');
 		if ($this->includeIdentifiers) $this->logOrEcho('Occurrence Alternative Identifiers exported as a Identifier extension file... ');
+		if ($this->includeAssociations) $this->logOrEcho('Occurrence Associations exported as a Resource Relationship extension file... ');
 		return $filePath;
 	}
 
@@ -2063,6 +2106,22 @@ private function writeIdentifierData($batchOccidArr){
 		if($this->identierHandler) $this->identierHandler->writeOutRecordBlock($batchOccidArr);
 	}
 
+	private function writeAssociationData($batchOccidArr){
+		if(!$this->associationHandler){
+			$this->associationHandler = new DwcArchiverResourceRelationship($this->conn);
+			$this->associationHandler->setSchemaType($this->schemaType);
+			$this->associationHandler->initiateProcess($this->targetPath . $this->ts . '-assoc' . $this->fileExt);
+			$this->fieldArrMap['associations'] = $this->associationHandler->getFieldArrTerms();
+		}
+		if($this->associationHandler){
+			$this->associationHandler->writeOutRecordBlock($batchOccidArr, 'oa.occid');
+			//Now add inverse relationships
+			$this->associationHandler->setSqlBase(true);
+			$this->associationHandler->writeOutRecordBlock($batchOccidArr, 'oa.occidAssociate');
+
+		}
+	}
+
 	private function writeCitationFile(){
 		$this->logOrEcho("Creating citation file (" . date('h:i:s A') . ")... ");
 		$filePath = $this->targetPath . $this->ts . '-citation.txt';
@@ -2247,6 +2306,11 @@ public function setIncludeIdentifiers($include){
 		else $this->includeIdentifiers = false;
 	}
 
+	public function setIncludeAssociations($include){
+		if($include) $this->includeAssociations = true;
+		else $this->includeAssociations = false;
+	}
+
 	public function hasAttributes($collid = false){
 		$bool = false;
 		$sql = 'SELECT occid FROM tmattributes LIMIT 1';
@@ -2284,6 +2348,30 @@ public function hasIdentifiers($collid = false){
 		return $bool;
 	}
 
+	public function hasAssociations($collid = false){
+		$bool = false;
+		$sql = 'SELECT occid FROM omoccurassociations LIMIT 1';
+		if(is_numeric($collid)){
+			$sql = "(SELECT o.occid FROM omoccurrences o INNER JOIN omoccurassociations a ON o.occid = a.occid WHERE o.collid = ?) UNION (SELECT o.occid FROM omoccurrences o INNER JOIN omoccurassociations a ON o.occid = a.occidAssociate WHERE o.collid = ?) LIMIT 1;";
+		}
+		$stmt = $this->conn->stmt_init();
+		if (!$stmt->prepare($sql)) {
+        	throw new Exception("SQL Error: " . $stmt->error);
+    	}
+		if (is_numeric($collid)) {
+			$stmt->bind_param('ii',$collid,$collid);
+		}
+		$stmt->execute();
+		$result = $stmt->get_result();
+		if ($result && $result->num_rows > 0) {
+			$bool = true;
+		}
+		$result->free();
+    	$stmt->close();
+
+		return $bool;
+	}
+
 	public function setRedactLocalities($redact){
 		$this->redactLocalities = $redact;
 	}

classes/DwcArchiverOccurrence.php

@@ -138,8 +138,8 @@ public function getOccurrenceArr(){
 		$this->occurDefArr['fields']['dataGeneralizations'] = 'o.dataGeneralizations';
 		$this->occurDefArr['terms']['dynamicProperties'] = 'http://rs.tdwg.org/dwc/terms/dynamicProperties';
 		$this->occurDefArr['fields']['dynamicProperties'] = 'o.dynamicProperties';
-		$this->occurDefArr['terms']['associatedOccurrences'] = 'http://rs.tdwg.org/dwc/terms/associatedOccurrences';
-		$this->occurDefArr['fields']['associatedOccurrences'] = '';
+		// $this->occurDefArr['terms']['associatedOccurrences'] = 'http://rs.tdwg.org/dwc/terms/associatedOccurrences';
+		// $this->occurDefArr['fields']['associatedOccurrences'] = '';
 		$this->occurDefArr['terms']['associatedSequences'] = 'http://rs.tdwg.org/dwc/terms/associatedSequences';
 		$this->occurDefArr['fields']['associatedSequences'] = '';
 		$this->occurDefArr['terms']['associatedTaxa'] = 'http://rs.tdwg.org/dwc/terms/associatedTaxa';
@@ -471,7 +471,7 @@ public function getAssociationStr($occid, $associationType = null){
 				$rs->free();
 			}
 			//Append associations of duplicate specimen
-			$this->appendSpecimenDuplicateAssociations($occid, $assocArr, $internalAssocOccidArr);
+			// $this->appendSpecimenDuplicateAssociations($occid, $assocArr, $internalAssocOccidArr);
 
 			//Append resource URLs to each output record
 			if($internalAssocOccidArr){

classes/DwcArchiverPublisher.php

@@ -54,6 +54,7 @@ public function batchCreateDwca($collIdArr){
 		$includeAttributes = $this->includeAttributes;
 		$includeMatSample = $this->includeMaterialSample;
 		$includeIdentifiers = $this->includeIdentifiers;
+		$includeAssociations = $this->includeAssociations;
 		foreach($collIdArr as $id){
 			//Create a separate DWCA object for each collection
 			if($includeAttributes){
@@ -68,6 +69,10 @@ public function batchCreateDwca($collIdArr){
 				if($this->hasIdentifiers($id)) $this->includeIdentifiers = true;
 				else $this->includeIdentifiers = false;
 			}
+			if($includeAssociations){
+				if($this->hasAssociations($id)) $this->includeAssociations = true;
+				else $this->includeAssociations = false;
+			}
 			$this->resetCollArr($id);
 			$this->conditionArr['collid'] = $id;
 			$this->conditionSql = '';
@@ -79,6 +84,7 @@ public function batchCreateDwca($collIdArr){
 		$this->includeAttributes = $includeAttributes;
 		$this->includeMaterialSample = $includeMatSample;
 		$this->includeIdentifiers = $includeIdentifiers;
+		$this->includeAssociations = $includeAssociations;
 		//Reset $this->collArr with all the collections ran successfully and then rebuild the RSS feed
 		$this->resetCollArr(implode(',',$successArr));
 		$this->writeRssFile();