6.20.0

classes/CronManager.php

@@ -743,7 +743,7 @@ public function runBatchJobs($numRunBeforeInCron = 0) {
                                 && ($numRunBeforeInCron <= self::MAX_BATCHES_IN_ONE_CRON)
                             ) {
                                 sleep(1);
-                                Application::log("Flight Tracker repeating cron", $firstBatchQueue['pid']);
+                                Application::log("Flight Tracker repeating cron $this->title", $firstBatchQueue['pid']);
                                 $this->runBatchJobs($numRunBeforeInCron);
                             }
                         } else {
@@ -762,6 +762,10 @@ public function runBatchJobs($numRunBeforeInCron = 0) {
                     $this->saveBatchQueueToDB($batchQueue);
                     return;
                 }
+				if (!$queueHasRun) {
+					sleep(60);
+					Application::log("End of CronManager.php While Loop $this->title");
+				}
             } while (!$queueHasRun);
         } else if (!in_array($firstBatchQueue['status'], $validBatchStatuses)) {
             throw new \Exception("Improper batch status ".$firstBatchQueue['status']);

classes/DateManagement.php

@@ -404,6 +404,7 @@ public static function getMonthNumber($monthStr) {
             "FALL" => "09",
             "AUTUMN" => "09",
             "WINTER" => "12",
+            "SPECIAL" => "01"
         ];
         for ($i = 1; $i <= 12; $i++) {
             $month = REDCapManagement::padInteger($i, 2);

classes/FileManagement.php

@@ -5,12 +5,16 @@
 use Dompdf\Dompdf;
 use Dompdf\Options;
 
+
 require_once(__DIR__ . '/ClassLoader.php');
 if (file_exists(__DIR__ . '/../vendor/autoload.php')) {
     require_once(__DIR__ . '/../vendor/autoload.php');
 }
 
 class FileManagement {
+
+	public CONST MAX_DOWNLOAD_FILE_SIZE = 20000000; //20 Megabytes
+
     public static function makePDFToTempFile($html) {
         $options = new Options();
         $options->set('tempDir', preg_replace("/\/$/", "", APP_PATH_TEMP));   // for images
@@ -158,19 +162,23 @@ public static function getMimeSuffix($mimeType) {
     public static function getEdocBase64($id) {
         if (is_numeric($id)) {
             $module = Application::getModule();
-            $sql = "SELECT stored_name, mime_type FROM redcap_edocs_metadata WHERE doc_id = ?";
+            $sql = "SELECT stored_name, mime_type, doc_size FROM redcap_edocs_metadata WHERE doc_id = ?";
             $q = $module->query($sql, [$id]);
             if ($row = $q->fetch_assoc()) {
                 $filename = EDOC_PATH . $row['stored_name'];
                 $mimeType = $row['mime_type'];
-                if ($mimeType == "application/octet-stream") {
-                    if (preg_match("/\.svg$/", $row['stored_name'])) {
-                        $mimeType = "image/svg+xml";
-                    } else {
-                        $mimeType = mime_content_type($row['stored_name']) ?: $mimeType;
-                    }
-                }
-                return self::getBase64OfFile($filename, $mimeType);
+				$fileSize = $row['doc_size'];
+				if ($fileSize <= self::MAX_DOWNLOAD_FILE_SIZE) {
+					if ($mimeType == "application/octet-stream") {
+						if (preg_match("/\.svg$/", $row['stored_name'])) {
+							$mimeType = "image/svg+xml";
+						} else {
+							$mimeType = mime_content_type($row['stored_name']) ?: $mimeType;
+						}
+					}
+					return self::getBase64OfFile($filename, $mimeType);
+				}
+				return "";
             }
         }
         throw new \Exception("Invalid Edoc ID!");
@@ -193,4 +201,4 @@ public static function getEdoc($id) {
             return ["error" => "Could not find entry"];
         }
     }
-}
+}

classes/Portal.php

@@ -818,6 +818,8 @@ public function getStoredData() {
                 }
             } else if (!empty($storedData) && !self::isValidStoredDate($storedDate)) {
                 Application::saveSystemSetting($this->username, []);
+            } else {
+				return $storedData;
             }
         }
         return [];
@@ -952,8 +954,9 @@ public function getModifyPhotoPage() {
         }
         $html .= "<form action='{$this->driverURL}' method='POST' enctype='multipart/form-data' id='photoForm'>";
         $html .= "<input type='hidden' name='action' value='upload_photo' />";
-        $html .= "<p class='centered'><label for='photoFile'>Photo:</label> <input type='file' id='photoFile' name='photoFile' onchange='portal.validateFile(this);' /><br/>";
-        $html .= self::makePortalButton("portal.uploadPhoto(\"#photoForm\");", "Upload");
+		$html .= "<p class='centered'><label for='photoFile'>Photo:</label> <input type='file' id='photoFile' name='photoFile' onchange='portal.validateFile(this);' /><br/>";
+        $html .= Application::generateCSRFTokenHTML();
+		$html .= self::makePortalButton("portal.uploadPhoto(\"#photoForm\");", "Upload");
         $html .= "</form>";
         return $html;
     }

classes/Publications.php

@@ -2489,7 +2489,7 @@ public static function getCitationsFromPubMed(array $pmids, array $metadata, str
                                 $upload[$j]["citation_field_citation_rate"] = $iCite->getVariable($pmid, "field_citation_rate");
                                 $upload[$j]["citation_nih_percentile"] = $iCite->getVariable($pmid, "nih_percentile");
                                 $upload[$j]["citation_rcr"] = $iCite->getVariable($pmid, "relative_citation_ratio");
-                                if (in_array("citation_referencing", $metadataFields)) {
+                                if (in_array("citation_icite_referencing", $metadataFields)) {
                                     $sep = ", ";
                                     $upload[$j]["citation_icite_cited_by_clinical"] = implode($sep, $iCite->getVariable($pmid, "cited_by_clin") ?: []);
                                     $upload[$j]["citation_icite_cited_by"] = implode($sep, $iCite->getVariable($pmid, "cited_by") ?: []);

classes/RePORTER.php

@@ -564,7 +564,7 @@ public static function updateEndDates($token, $server, $pid, $records, $prefix,
             $awardNoWithInstances = [];
             $redcapData = Download::fieldsForRecords($token, $server, $fieldsToDownload, [$recordId]);
             foreach ($redcapData as $row) {
-                if ($row["redcap_repeat_instrument"] == $instrument) {
+                if (array_key_exists("redcap_repeat_instrument", $row) && $row["redcap_repeat_instrument"] == $instrument) {
                     if (!isset($awardNoWithInstances[$row[$awardNoField]])) {
                         $awardNoWithInstances[$row[$awardNoField]] = [];
                     }
@@ -825,8 +825,12 @@ private function filterForExcludeList() {
                             $pi['last_name']." ".$pi['first_name'],
                             $pi['last_name'].", ".$pi['first_name'],
                         ];
+                        if ($pi['middle_name'] ?? FALSE) {
+                            $piNames[] = $pi['first_name']." ".$pi['middle_name']." ".$pi['last_name'];
+                            $piNames[] = $pi['last_name'].", ".$pi['first_name']." ".$pi['middle_name'];
+                        }
                         foreach ($piNames as $piName) {
-                            if ($piName == $excludeName) {
+                            if (strtolower($piName) == strtolower($excludeName)) {
                                 $excludeThisItem = TRUE;
                                 break;
                             }
@@ -890,4 +894,4 @@ private function isFederal() {
     private $category;
     private $includeFields;
     private $excludeList;
-}
+}

classes/ReactNIHTables.php

@@ -154,7 +154,7 @@ private function makeModificationsArray($lookupValues, $data, $headers, $tableNu
     public function sendVerificationEmail($post, &$nihTables) {
         $email = strtolower(Sanitizer::sanitize($post['email']));
         $scholarEmail = strtolower(Sanitizer::sanitize($post['scholarEmail']));
-        if (!REDCapManagement::isEmailOrEmails($email) || !REDCapManagement::isEmailOrEmails($scholarEmail)) {
+        if (!REDCapManagement::isEmailOrEmails($email) && !REDCapManagement::isEmailOrEmails($scholarEmail)) {
             return ["error" => "Improper email"];
         }
         $name = Sanitizer::sanitize($post['name'] ?? "");