Merge pull request #29 from BioKIC/master

code update
BioKIC · Jun 16, 2022 · 9332ccb · 9332ccb
2 parents a7af515 + 743f6ea
commit 9332ccb
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Showing 41 changed files with 1,392 additions and 950 deletions.
diff --git a/admin/portalindex.php b/admin/portalindex.php
@@ -8,11 +8,13 @@
 
 $portalID = array_key_exists('portalid',$_REQUEST)?$_REQUEST['portalid']:0;
 $remoteID = array_key_exists('remoteid',$_REQUEST)?$_REQUEST['remoteid']:0;
+$remotePath = array_key_exists('remotePath',$_POST)?$_POST['remotePath']:'';
 $formSubmit = array_key_exists('formsubmit',$_POST)?$_POST['formsubmit']:'';
 
 //Sanitation
 if(!is_numeric($portalID)) $portalID = 0;
 if(!is_numeric($remoteID)) $remoteID = 0;
+$remotePath = filter_var($remotePath, FILTER_SANITIZE_URL);
 
 $portalManager = new PortalIndex();
 
@@ -29,13 +31,21 @@
 		<script src="<?php echo $CLIENT_ROOT; ?>/js/jquery.js" type="text/javascript"></script>
 		<script src="<?php echo $CLIENT_ROOT; ?>/js/jquery-ui.js" type="text/javascript"></script>
 		<script type="text/javascript">
+			function validateHandshakeForm(f){
+				if(f.remotePath.value == ""){
+					alert("Enter URL to remote portal base index page");
+					return false;
+				}
+				return true;
+			}
 		</script>
 		<style type="text/css">
 			fieldset{ margin:20px; padding:15px; }
 			legend{ font-weight: bold; }
 			label{  }
 			button{ margin: 20px; }
 			hr{ margin-top: 15px; margin-bottom: 15px; }
+			.field-row{  }
 		</style>
 	</head>
 	<body>
@@ -49,16 +59,53 @@
 		</div>
 		<div id="innertext">
 			<?php
-			if($isEditor){
-				if($formSubmit == 'importProfile'){
-					if($collid = $portalManager->importProfile($portalID, $remoteID)) echo '<div><a href="../collections/misc/collprofiles.php?collid='.$collid.'" target="_blank">New snapshot collection created</a></div>';
-					else echo '<div>failed to insert new collections: '.$portalManager->getErrorMessage().'</div>';
+			if(!isset($GLOBALS['ACTIVATE_PORTAL_INDEX'])){
+				echo 'This feature has not yet been activated within this portal';
+			}
+			elseif($isEditor){
+				if($formSubmit && $formSubmit != 'listCollections'){
+					echo '<fieldset>';
+					echo '<legend>Action Panel</legend>';
+					if($formSubmit == 'importProfile'){
+						if($collid = $portalManager->importProfile($portalID, $remoteID)) echo '<div><a href="../collections/misc/collprofiles.php?collid='.$collid.'" target="_blank">New snapshot collection created</a></div>';
+						else echo '<div>failed to insert new collections: '.$portalManager->getErrorMessage().'</div>';
+					}
+					elseif($formSubmit == 'initiateHandshake'){
+						if($resArr = $portalManager->initiateHandshake($remotePath)){
+							if($resArr['status']) echo '<div>Success - handshake successful: '.$resArr['message'].'</div>';
+							else echo '<div>ERROR - handshake failed: '.$resArr['message'].'</div>';
+							//print_r($resArr);
+						}
+						else echo '<div>ERROR initiating handshake: '.$portalManager->getErrorMessage().'</div>';
+					}
+					echo '</fieldset>';
+				}
+				$selfArr = $portalManager->getSelfDetails();
+				if($formSubmit != 'listCollections'){
+					?>
+					<fieldset>
+						<legend>Current Portal Details</legend>
+						<div class="field-row"><label>Portal title:</label> <?php echo $selfArr['portalName']; ?></div>
+						<div class="field-row"><label>Root URL:</label> <?php echo $selfArr['urlRoot']; ?></div>
+						<div class="field-row"><label>Global Unique Identifier:</label> <?php echo $selfArr['guid']; ?></div>
+						<div class="field-row"><label>Manager email:</label> <?php echo $selfArr['managerEmail']; ?></div>
+						<div class="field-row"><label>Software version:</label> <?php echo $selfArr['symbiotaVersion']; ?></div>
+						<hr />
+						<div class="handshake-div"><a href="#" onclick="$('.handshake-div').toggle(); return false;">Initiate Handshake with External Portal</a></div>
+						<div class="handshake-div" style="display:none">
+							<form action="portalindex.php" method="post" onsubmit="return validateHandshakeForm(this)">
+								<div class="field-row"><label>Path to Remote Portal:</label> <input name="remotePath" type="text" value="<?php echo $remotePath; ?>" style="width: 500px" /></div>
+								<div class="field-row"><button name="formsubmit" type="submit" value="initiateHandshake">Initiate Handshake</button></div>
+							</form>
+						</div>
+					</fieldset>
+					<?php
 				}
-				$indexArr = $portalManager->getPortalIndexArr($portalID);
 				?>
 				<fieldset>
 					<legend>Portal Index</legend>
 					<?php
+					$indexArr = $portalManager->getPortalIndexArr($portalID);
 					foreach($indexArr as $portalID => $portalArr){
 						foreach($portalArr as $fieldName => $fieldValue){
 							if($fieldValue){
@@ -160,6 +207,7 @@
 						}
 						echo '<hr/>';
 					}
+					if(!$indexArr) echo '<div>Portal Index empty. No portals have yet been registered.</div>';
 					?>
 				</fieldset>
 				<?php

diff --git a/api/app/Http/Controllers/InstallationController.php b/api/app/Http/Controllers/InstallationController.php
@@ -196,12 +196,15 @@ public function portalHandshake($id, Request $request){
 								foreach($remoteInstallationArr['results'] as $portal){
 									if(PortalIndex::where('guid',$portal['guid'])->count()) $currentRegistered++;
 									elseif($portal['guid'] != $_ENV['PORTAL_GUID']){
-										//Add remote
-										PortalIndex::create($portal);
-										//Touch remote installation but don't wait for a response because propagation across a large network can take awhile
-										$urlTouch = $portal['urlRoot'].'/api/v2/installation/'.$_ENV['PORTAL_GUID'].'/touch?endpoint='.htmlentities($this->getServerDomain().$_ENV['CLIENT_ROOT']);
-										$this->getAPIResponce($urlTouch, true);
-										$newRegistration++;
+										//If remote exists, add by retriving info directly from source
+										$remotePing = $portal['urlRoot'].'/api/v2/installation/ping';
+										if($newRemote = $this->getAPIResponce($remotePing)){
+											PortalIndex::create($newRemote);
+											//Touch remote installation but don't wait for a response because propagation across a large network can take awhile
+											$urlTouch = $portal['urlRoot'].'/api/v2/installation/'.$_ENV['PORTAL_GUID'].'/touch?endpoint='.htmlentities($this->getServerDomain().$_ENV['CLIENT_ROOT']);
+											$this->getAPIResponce($urlTouch, true);
+											$newRegistration++;
+										}
 									}
 								}
 								$responseArr['Current registered remotes obtained from remote library'] = $currentRegistered;
@@ -306,6 +309,10 @@ public function showOccurrences($id, Request $request){
 
 	public function create(Request $request){
 		/*
+		$validated = $request->validate([
+			'portalName' => 'required|max:45',
+			'urlRoot' => 'required|max:150',
+		]);
 		$portalIndex = PortalIndex::create($request->all());
 
 		return response()->json($portalIndex, 201);

diff --git a/api/vendor/laravel/lumen-framework/config/database.php b/api/vendor/laravel/lumen-framework/config/database.php
@@ -142,11 +142,15 @@
 		require_once($symbBasePath.'/config/dbconnection.php');
 		foreach(MySQLiConnectionFactory::$SERVERS as $dbArr){
 			if($dbArr['type'] = 'write'){
-				$params['connections']['mysql']['host'] = $dbArr['host'];
-				$params['connections']['mysql']['port'] = $dbArr['port'];
+				$host = 'localhost';
+				if(isset($dbArr['host'])) $host = $dbArr['host'];
+				$params['connections']['mysql']['host'] = $host;
 				$params['connections']['mysql']['database'] = $dbArr['database'];
 				$params['connections']['mysql']['username'] = $dbArr['username'];
 				$params['connections']['mysql']['password'] = $dbArr['password'];
+				$port = '3306';
+				if(isset($dbArr['port'])) $port = $dbArr['port'];
+				$params['connections']['mysql']['port'] = $port;
 			}
 		}
 	}

diff --git a/api/vendor/psr/log/src/LoggerInterface.php b/api/vendor/psr/log/src/LoggerInterface.php
@@ -27,7 +27,7 @@ interface LoggerInterface
      *
      * @return void
      */
-    public function emergency(string|\Stringable $message, array $context = []);
+    public function emergency(string $message, array $context = []);
 
     /**
      * Action must be taken immediately.
@@ -40,7 +40,7 @@ public function emergency(string|\Stringable $message, array $context = []);
      *
      * @return void
      */
-    public function alert(string|\Stringable $message, array $context = []);
+    public function alert(string $message, array $context = []);
 
     /**
      * Critical conditions.
@@ -52,7 +52,7 @@ public function alert(string|\Stringable $message, array $context = []);
      *
      * @return void
      */
-    public function critical(string|\Stringable $message, array $context = []);
+    public function critical(string $message, array $context = []);
 
     /**
      * Runtime errors that do not require immediate action but should typically
@@ -63,7 +63,7 @@ public function critical(string|\Stringable $message, array $context = []);
      *
      * @return void
      */
-    public function error(string|\Stringable $message, array $context = []);
+    public function error(string $message, array $context = []);
 
     /**
      * Exceptional occurrences that are not errors.
@@ -76,7 +76,7 @@ public function error(string|\Stringable $message, array $context = []);
      *
      * @return void
      */
-    public function warning(string|\Stringable $message, array $context = []);
+    public function warning(string $message, array $context = []);
 
     /**
      * Normal but significant events.
@@ -86,7 +86,7 @@ public function warning(string|\Stringable $message, array $context = []);
      *
      * @return void
      */
-    public function notice(string|\Stringable $message, array $context = []);
+    public function notice(string $message, array $context = []);
 
     /**
      * Interesting events.
@@ -98,7 +98,7 @@ public function notice(string|\Stringable $message, array $context = []);
      *
      * @return void
      */
-    public function info(string|\Stringable $message, array $context = []);
+    public function info(string $message, array $context = []);
 
     /**
      * Detailed debug information.
@@ -108,7 +108,7 @@ public function info(string|\Stringable $message, array $context = []);
      *
      * @return void
      */
-    public function debug(string|\Stringable $message, array $context = []);
+    public function debug(string $message, array $context = []);
 
     /**
      * Logs with an arbitrary level.
@@ -121,5 +121,5 @@ public function debug(string|\Stringable $message, array $context = []);
      *
      * @throws \Psr\Log\InvalidArgumentException
      */
-    public function log($level, string|\Stringable $message, array $context = []);
+    public function log($level, string $message, array $context = []);
 }
diff --git a/checklists/checklistadmin.php b/checklists/checklistadmin.php
@@ -14,13 +14,20 @@
 if(!$clid && isset($_POST['delclid'])) $clid = $_POST['delclid'];
 $clManager->setClid($clid);
 
+
+$statusStr = '';
 if($action == 'SubmitAdd'){
-	//Anyone with a login can create a checklist
-	$newClid = $clManager->createChecklist($_POST);
-	header('Location: checklist.php?clid='.$newClid);
+
+	//Conform User Checklist permission 
+	if($IS_ADMIN || (array_key_exists('ClAdmin',$USER_RIGHTS) && in_array($clid,$USER_RIGHTS['ClAdmin'])) || array_key_exists('ClCreate',$USER_RIGHTS)){		
+		$newClid = $clManager->createChecklist($_POST);
+		header('Location: checklist.php?clid='.$newClid);
+	} 
+
+	//If we made it here the user does not have any checklist roles. cancel further execution.
+	$statusStr = 'You do not have permission to create a Checklist.';
 }
 
-$statusStr = '';
 $isEditor = 0;
 if($IS_ADMIN || (array_key_exists('ClAdmin',$USER_RIGHTS) && in_array($clid,$USER_RIGHTS['ClAdmin']))){
 	$isEditor = 1;
@@ -58,7 +65,7 @@
 }
 $clArray = $clManager->getMetaData();
 $defaultArr = array();
-if($clArray['defaultsettings']){
+if(array_key_exists('defaultsettings',$clArray)){
 	$defaultArr = json_decode($clArray['defaultsettings'], true);
 }
 ?>

diff --git a/checklists/clgmap.php b/checklists/clgmap.php
@@ -7,6 +7,9 @@
 $pid = $_REQUEST['pid'];
 $target = array_key_exists('target',$_REQUEST)?$_REQUEST['target']:'checklists';
 
+//Sanitation
+if(!is_numeric($pid)) $pid = 0;
+
 $clManager = new ChecklistManager();
 $clManager->setProj($pid);
 ?>

diff --git a/checklists/clsppeditor.php b/checklists/clsppeditor.php
@@ -4,10 +4,15 @@
 @include_once($SERVER_ROOT.'/content/lang/checklists/clsppeditor.'.$LANG_TAG.'.php');
 header("Content-Type: text/html; charset=".$CHARSET);
 
-$clid = array_key_exists("clid",$_REQUEST)?$_REQUEST["clid"]:"";
-$tid = array_key_exists("tid",$_REQUEST)?$_REQUEST["tid"]:"";
-$tabIndex = array_key_exists("tabindex",$_POST)?$_POST["tabindex"]:0;
-$action = array_key_exists("action",$_POST)?$_POST["action"]:"";
+$clid = array_key_exists('clid',$_REQUEST)?$_REQUEST['clid']:0;
+$tid = array_key_exists('tid',$_REQUEST)?$_REQUEST['tid']:0;
+$tabIndex = array_key_exists('tabindex',$_POST)?$_POST['tabindex']:0;
+$action = array_key_exists('action',$_POST)?$_POST['action']:'';
+
+//Sanitation
+if(!is_numeric($clid)) $clid = 0;
+if(!is_numeric($tid)) $tid = 0;
+if(!is_numeric($tabIndex)) $tabIndex = 0;
 
 $isEditor = false;
 if($IS_ADMIN || (array_key_exists("ClAdmin",$USER_RIGHTS) && in_array($clid,$USER_RIGHTS["ClAdmin"]))){

diff --git a/classes/DwcArchiverCore.php b/classes/DwcArchiverCore.php
@@ -99,7 +99,6 @@ public function getOccurrenceCnt(){
 		//if($this->schemaType != 'backup') $sql .= ' LIMIT 1000000';
 		if($sql){
 			$sql = 'SELECT COUNT(o.occid) as cnt '.$sql;
-			//echo $sql; exit;
 			$rs = $this->conn->query($sql);
 			while($r = $rs->fetch_object()){
 				$retStr = $r->cnt;
@@ -292,6 +291,7 @@ private function applyConditions(){
 					$taxaManager = new OccurrenceTaxaManager();
 					$taxaArr = array();
 					$taxaArr['taxa'] = implode(';',$condArr['EQUALS']);
+					if($field == 'family') $taxaArr['taxontype'] = 3;
 					$taxaManager->setTaxonRequestVariable($taxaArr);
 					$sqlFrag .= $taxaManager->getTaxonWhereFrag();
 				}
@@ -1641,20 +1641,23 @@ private function writeOccurrenceFile(){
 			if($collidStr) $this->setCollArr(trim($collidStr,','));
 		}
 
-		//$dwcOccurManager->setUpperTaxonomy();
-		$dwcOccurManager->setTaxonRank();
-
 		$materialSampleHandler = null;
-		if($this->includeMaterialSample){
-			$collid = key($this->collArr);
-			if(isset($this->collArr[$collid]['matSample'])){
-				$this->logOrEcho('Creating material sample extension file ('.date('h:i:s A').')... ');
-				$materialSampleHandler = new DwcArchiverMaterialSample($this->conn);
-				$materialSampleHandler->initiateProcess($this->targetPath.$this->ts.'-matSample'.$this->fileExt);
-				$materialSampleHandler->setSchemaType($this->schemaType);
-				$this->fieldArrMap['materialSample'] = $materialSampleHandler->getFieldArrTerms();
+		if($this->schemaType != 'coge'){
+			//$dwcOccurManager->setUpperTaxonomy();
+			$dwcOccurManager->setTaxonRank();
+
+			if($this->includeMaterialSample){
+				$collid = key($this->collArr);
+				if(isset($this->collArr[$collid]['matSample'])){
+					$this->logOrEcho('Creating material sample extension file ('.date('h:i:s A').')... ');
+					$materialSampleHandler = new DwcArchiverMaterialSample($this->conn);
+					$materialSampleHandler->initiateProcess($this->targetPath.$this->ts.'-matSample'.$this->fileExt);
+					$materialSampleHandler->setSchemaType($this->schemaType);
+					$this->fieldArrMap['materialSample'] = $materialSampleHandler->getFieldArrTerms();
+				}
 			}
 		}
+
 		//echo $sql; exit;
 		if($rs = $this->dataConn->query($sql,MYSQLI_USE_RESULT)){
 			$this->setServerDomain();
@@ -1738,22 +1741,23 @@ private function writeOccurrenceFile(){
 				elseif($this->schemaType == 'backup') unset($r['collID']);
 
 				if($ocnStr = $dwcOccurManager->getAdditionalCatalogNumberStr($r['occid'])) $r['otherCatalogNumbers'] = $ocnStr;
-				if($exsArr = $dwcOccurManager->getExsiccateArr($r['occid'])){
-					$exsStr = $exsArr['exsStr'];
-					if(isset($r['occurrenceRemarks']) && $r['occurrenceRemarks']) $exsStr = $r['occurrenceRemarks'].'; '.$exsStr;
-					$r['occurrenceRemarks'] = $exsStr;
-					$dynProp = 'exsiccatae: '.$exsArr['exsJson'];
-					if(isset($r['dynamicProperties']) && $r['dynamicProperties']) $dynProp = $r['dynamicProperties'].'; '.$dynProp;
-					$r['dynamicProperties'] = $dynProp;
+				if($this->schemaType != 'coge'){
+					if($exsArr = $dwcOccurManager->getExsiccateArr($r['occid'])){
+						$exsStr = $exsArr['exsStr'];
+						if(isset($r['occurrenceRemarks']) && $r['occurrenceRemarks']) $exsStr = $r['occurrenceRemarks'].'; '.$exsStr;
+						$r['occurrenceRemarks'] = $exsStr;
+						$dynProp = 'exsiccatae: '.$exsArr['exsJson'];
+						if(isset($r['dynamicProperties']) && $r['dynamicProperties']) $dynProp = $r['dynamicProperties'].'; '.$dynProp;
+						$r['dynamicProperties'] = $dynProp;
+					}
+					if($assocOccurStr = $dwcOccurManager->getAssociationStr($r['occid'])) $r['t_associatedOccurrences'] = $assocOccurStr;
+					if($assocSeqStr = $dwcOccurManager->getAssociatedSequencesStr($r['occid'])) $r['t_associatedSequences'] = $assocSeqStr;
+					if($assocTaxa = $dwcOccurManager->getAssocTaxa($r['occid'])) $r['associatedTaxa'] = $assocTaxa;
 				}
-				if($assocOccurStr = $dwcOccurManager->getAssociationStr($r['occid'])) $r['t_associatedOccurrences'] = $assocOccurStr;
-				if($assocSeqStr = $dwcOccurManager->getAssociatedSequencesStr($r['occid'])) $r['t_associatedSequences'] = $assocSeqStr;
-				if($assocTaxa = $dwcOccurManager->getAssocTaxa($r['occid'])) $r['associatedTaxa'] = $assocTaxa;
 				//$dwcOccurManager->appendUpperTaxonomy($r);
 				$dwcOccurManager->appendUpperTaxonomy2($r);
 				if($rankStr = $dwcOccurManager->getTaxonRank($r['rankid'])) $r['t_taxonRank'] = $rankStr;
 				unset($r['rankid']);
-
 				$this->encodeArr($r);
 				$this->addcslashesArr($r);
 				$this->writeOutRecord($fh,$r);
@@ -2139,10 +2143,10 @@ public function setServerDomain($domain = ''){
 			$this->serverDomain = $domain;
 		}
 		elseif(!$this->serverDomain){
-			$this->serverDomain = "http://";
-			if((!empty($_SERVER['HTTPS']) && $_SERVER['HTTPS'] !== 'off') || $_SERVER['SERVER_PORT'] == 443) $this->serverDomain = "https://";
-			$this->serverDomain .= $_SERVER["SERVER_NAME"];
-			if($_SERVER["SERVER_PORT"] && $_SERVER["SERVER_PORT"] != 80 && $_SERVER['SERVER_PORT'] != 443) $this->serverDomain .= ':'.$_SERVER["SERVER_PORT"];
+			$this->serverDomain = 'http://';
+			if((!empty($_SERVER['HTTPS']) && $_SERVER['HTTPS'] !== 'off') || $_SERVER['SERVER_PORT'] == 443) $this->serverDomain = 'https://';
+			$this->serverDomain .= $_SERVER['SERVER_NAME'];
+			if($_SERVER['SERVER_PORT'] && $_SERVER['SERVER_PORT'] != 80 && $_SERVER['SERVER_PORT'] != 443) $this->serverDomain .= ':'.$_SERVER['SERVER_PORT'];
 		}
 	}