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Merge pull request #10 from BioKIC/master
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Merge BioKIC/Symbiota developments
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@egbot
egbot authored Jun 16, 2022
2 parents 24288ef + 743f6ea commit b1dc2ee
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Showing 26 changed files with 865 additions and 668 deletions.
41 changes: 26 additions & 15 deletions admin/portalindex.php
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Original file line number Diff line number Diff line change
Expand Up @@ -59,8 +59,11 @@ function validateHandshakeForm(f){
</div>
<div id="innertext">
<?php
if($isEditor){
if($formSubmit){
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'){
Expand All @@ -78,20 +81,27 @@ function validateHandshakeForm(f){
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
}
?>
<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 />
<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 $remotePath; ?>" style="width: 500px" /></div>
<div class="field-row"><button name="formsubmit" type="submit" value="initiateHandshake">Initiate Handshake</button></div>
</form>
</fieldset>
<fieldset>
<legend>Portal Index</legend>
<?php
Expand Down Expand Up @@ -197,6 +207,7 @@ function validateHandshakeForm(f){
}
echo '<hr/>';
}
if(!$indexArr) echo '<div>Portal Index empty. No portals have yet been registered.</div>';
?>
</fieldset>
<?php
Expand Down
19 changes: 13 additions & 6 deletions api/app/Http/Controllers/InstallationController.php
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Original file line number Diff line number Diff line change
Expand Up @@ -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'] = $currentRegistered;
Expand Down Expand Up @@ -306,6 +309,10 @@ public function showOccurrences($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($portalIndex, 201);
Expand Down
8 changes: 6 additions & 2 deletions api/vendor/laravel/lumen-framework/config/database.php
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Original file line number Diff line number Diff line change
Expand Up @@ -142,11 +142,15 @@
require_once($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;
}
}
}
Expand Down
18 changes: 9 additions & 9 deletions api/vendor/psr/log/src/LoggerInterface.php
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Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand All @@ -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.
Expand All @@ -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
Expand All @@ -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.
Expand All @@ -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.
Expand All @@ -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.
Expand All @@ -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.
Expand All @@ -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.
Expand All @@ -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 $context = []);
}
17 changes: 12 additions & 5 deletions checklists/checklistadmin.php
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Original file line number Diff line number Diff line change
Expand Up @@ -14,13 +14,20 @@
if(!$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;
Expand Down Expand Up @@ -58,7 +65,7 @@
}
$clArray = $clManager->getMetaData();
$defaultArr = array();
if($clArray['defaultsettings']){
if(array_key_exists('defaultsettings',$clArray)){
$defaultArr = json_decode($clArray['defaultsettings'], true);
}
?>
Expand Down
3 changes: 3 additions & 0 deletions checklists/clgmap.php
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
?>
Expand Down
13 changes: 9 additions & 4 deletions checklists/clsppeditor.php
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Original file line number Diff line number Diff line change
Expand Up @@ -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,$USER_RIGHTS["ClAdmin"]))){
Expand Down
38 changes: 20 additions & 18 deletions classes/OccurrenceAccessStats.php
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Original file line number Diff line number Diff line change
Expand Up @@ -65,28 +65,30 @@ public function batchRecordEventsBySql($sqlFrag, $accessType){
return $status;
}

private function insertAccessEvent($accessType, $queryStr){
public function insertAccessEvent($accessType, $queryStr){
$occurAccessID = false;
$remoteAddr = $_SERVER['REMOTE_ADDR'];
$userData = @get_browser();
if($userData) $userData = json_encode($userData);
else $userData = $_SERVER['HTTP_USER_AGENT'];
$sql = 'INSERT INTO omoccuraccess(ipAddress, accessType, queryStr, userAgent) VALUES(?, ?, ?, ?)';
$stmt = $this->conn->stmt_init();
$stmt->prepare($sql);
$stmt->bind_param('ssss', $remoteAddr, $accessType, $queryStr, $userData);
if($stmt->execute()){
$occurAccessID = $this->conn->insert_id;
}
else{
$this->errorMessage = date('Y-m-d H:i:s').' - ERROR creating access event: '.$this->conn->error;
$this->logOrEcho($this->errorMessage);
if(isset($GLOBALS['RECORD_STATS'])){
$remoteAddr = $_SERVER['REMOTE_ADDR'];
$userData = @get_browser();
if($userData) $userData = json_encode($userData);
else $userData = $_SERVER['HTTP_USER_AGENT'];
$sql = 'INSERT INTO omoccuraccess(ipAddress, accessType, queryStr, userAgent) VALUES(?, ?, ?, ?)';
$stmt = $this->conn->stmt_init();
$stmt->prepare($sql);
$stmt->bind_param('ssss', $remoteAddr, $accessType, $queryStr, $userData);
if($stmt->execute()){
$occurAccessID = $this->conn->insert_id;
}
else{
$this->errorMessage = date('Y-m-d H:i:s').' - ERROR creating access event: '.$this->conn->error;
$this->logOrEcho($this->errorMessage);
}
$stmt->close();
}
$stmt->close();
return $occurAccessID;
}

private function insertAccessOccurrence($occurAccessID, $occid){
public function insertAccessOccurrence($occurAccessID, $occid){
$status = false;
$sql = 'INSERT INTO omoccuraccesslink(occurAccessID, occid) VALUES(?, ?)';
$stmt = $this->conn->stmt_init();
Expand All @@ -104,7 +106,7 @@ private function insertAccessOccurrence($occurAccessID, $occid){
private function insertAccessOccurrenceBatch($occurAccessID, $sqlFrag){
$status = false;
if(is_numeric($occurAccessID)){
$sql = 'INSERT INTO omoccuraccessstats(occurAccessID, occid) SELECT '.$occurAccessID.', o.occid '.$sqlFrag;
$sql = 'INSERT INTO omoccuraccesslink(occurAccessID, occid) SELECT '.$occurAccessID.', o.occid '.$sqlFrag;
if($this->conn->query($sql)){
$status = true;
}
Expand Down
3 changes: 2 additions & 1 deletion classes/OccurrenceDownload.php
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Original file line number Diff line number Diff line change
Expand Up @@ -133,6 +133,7 @@ private function writeOutData($outstream){
$result = $this->conn->query($sql,MYSQLI_USE_RESULT);
if($result){
$statsManager = new OccurrenceAccessStats();
$occurAccessID = $statsManager->insertAccessEvent('download', substr($sql, strpos($sql, 'WHERE ')));
$outputHeader = true;
while($row = $result->fetch_assoc()){
if($outputHeader){
Expand All @@ -155,7 +156,7 @@ private function writeOutData($outstream){
}
//Set access statistics
if($this->isPublicDownload){
if($this->schemaType != 'checklist') if(array_key_exists('occid',$row)) $statsManager->recordAccessEvent($row['occid'], 'download');
if($this->schemaType != 'checklist') if(array_key_exists('occid',$row)) $statsManager->insertAccessOccurrence($occurAccessID, $row['occid']);
}
$recCnt++;
}
Expand Down
16 changes: 10 additions & 6 deletions classes/OccurrenceIndividual.php
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Original file line number Diff line number Diff line change
Expand Up @@ -701,13 +701,17 @@ public function getExternalEditArr(){

public function getAccessStats(){
$retArr = Array();
$sql = 'SELECT year(accessdate) as accessdate, accesstype, count(*) AS cnt FROM omoccuraccessstats WHERE (occid = '.$this->occid.') GROUP BY accessdate, accesstype';
//echo '<div>'.$sql.'</div>';
$rs = $this->conn->query($sql);
while($r = $rs->fetch_object()){
$retArr[$r->accessdate][$r->accesstype] = $r->cnt;
if(isset($GLOBALS['RECORD_STATS'])){
$sql = 'SELECT year(s.accessdate) as accessdate, s.accesstype, s.cnt
FROM omoccuraccesssummary s INNER JOIN omoccuraccesssummarylink l ON s.oasid = l.oasid
WHERE (l.occid = '.$this->occid.') GROUP BY s.accessdate, s.accesstype';
//echo '<div>'.$sql.'</div>';
$rs = $this->conn->query($sql);
while($r = $rs->fetch_object()){
$retArr[$r->accessdate][$r->accesstype] = $r->cnt;
}
$rs->free();
}
$rs->free();
return $retArr;
}

Expand Down
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