2.29.0

CareerDev.php

@@ -10,7 +10,7 @@ class CareerDev {
 	public static $passedModule = NULL;
 
 	public static function getVersion() {
-		return "2.28.1";
+		return "2.29.0";
 	}
 
 	public static function getLockFile($pid) {
@@ -99,7 +99,9 @@ public static function log($mssg, $pid = FALSE) {
 			if ($pid) {
 				$params = array("project_id" => $pid);
 				$module->log($mssg, $params);
-				// error_log($pid.": ".$mssg);
+				if (self::isVanderbilt()) {
+                    error_log($pid.": ".$mssg);
+                }
 			} else {
 				error_log($mssg);
 			}
@@ -585,6 +587,7 @@ public static function getMenu($menuName) {
             ];
             $ary["Configure an Email"] = self::link("/emailMgmt/configure.php");
             $ary["View Email Log"] = self::link("/emailMgmt/log.php");
+            $ary["View Email Queue"] = self::link("/emailMgmt/viewQueue.php");
             $ary["List of Nonrespondents"] = self::link("/emailMgmt/noSurvey.php");
             $ary["Survey Responses"] = self::link("/surveyResponses.php");
             $ary["Import General Data"] = self::link("/import.php");

FlightTrackerExternalModule.php

@@ -432,7 +432,7 @@ function cron() {
                 } else {
                     loadCrons($mgr, FALSE, $token, $server);
                 }
-                CareerDev::log($this->getName().": Running crons for pid $pid", $pid);
+                CareerDev::log($this->getName().": Running ".$mgr->getNumberOfCrons()." crons for pid $pid", $pid);
                 $addlEmailText = in_array($pid, $pidsUpdated) ? "Surveys shared from other Flight Tracker projects" : "";
                 $mgr->run($adminEmail, $tokenName, $addlEmailText);
                 CareerDev::log($this->getName().": cron run complete for pid $pid", $pid);

classes/Crons.php

@@ -12,10 +12,10 @@ public function __construct($token, $server, $pid) {
 		$this->server = $server;
 		$this->pid = $pid;
 
-		$this->crons = array();
+		$this->crons = [];
 		$days = self::getDaysOfWeek();
 		foreach ($days as $day) {
-			$this->crons[$day] = array();
+			$this->crons[$day] = [];
 		}
 
         $this->adminEmail = Application::getSetting("admin_email", $pid);
@@ -26,7 +26,8 @@ public function __construct($token, $server, $pid) {
 
 	# file is relative to career_dev's root
 	# dayOfWeek is in string format - "Monday", "Tuesday", etc. or a date in form Y-M-D
-	public function addCron($file, $method, $dayOfWeek) {
+    # records here, if specified, overrides the records specified in function run
+	public function addCron($file, $method, $dayOfWeek, $records = []) {
 		$possibleDays = self::getDaysOfWeek();
 		$dateTs = strtotime($dayOfWeek);
 		if (!in_array($dayOfWeek, $possibleDays) && !$dateTs) {
@@ -39,17 +40,29 @@ public function addCron($file, $method, $dayOfWeek) {
 		}
 
 		$cronjob = new CronJob($absFile, $method);
+        if (!empty($records)) {
+            $cronjob->setRecords($records);
+        }
+        // Application::log("Has day of week $dayOfWeek and timestamp for ".date("Y-m-d", $dateTs));
 		if (in_array($dayOfWeek, $possibleDays)) {
 			# Weekday
-			array_push($this->crons[$dayOfWeek], $cronjob);
+            if (!isset($this->crons[$dayOfWeek])) {
+                $this->crons[$dayOfWeek] = [];
+                // Application::log("Reset cron list for $dayOfWeek");
+            }
+			$this->crons[$dayOfWeek][] = $cronjob;
+            // Application::log("Assigned cron for $dayOfWeek");
 		} else if ($dateTs) {
 			# Y-M-D
 			$date = date(self::getDateFormat(), $dateTs);
 			if (!isset($this->crons[$date])) {
-				$this->crons[$date] = array();
+				$this->crons[$date] = [];
+				// Application::log("Reset cron list for $date");
 			}
-			array_push($this->crons[$date], $cronjob);
+			$this->crons[$date][] = $cronjob;
+			// Application::log("Assigned cron for $date");
 		}
+		// Application::log("Added cron $method: ".$this->getNumberOfCrons()." total crons now");
 	}
 
 	private static function getDaysOfWeek() {
@@ -95,31 +108,36 @@ public static function reportCronErrors() {
 		}
 	}
 
-	public function run($adminEmail = "", $tokenName = "", $additionalEmailText = "", $records = []) {
+	public function run($adminEmail = "", $tokenName = "", $additionalEmailText = "", $recordsToRun = []) {
 		$dayOfWeek = date("l");
 		$date = date(self::getDateFormat());
 		$keys = array($date, $dayOfWeek);     // in order that they will run
 
 		Application::log("CRONS RUN AT ".date("Y-m-d h:i:s")." FOR PID ".$this->pid);
 		Application::log("adminEmail ".$adminEmail);
-		$run = array();
-		$toRun = array();
+		Application::log("Looking in ".$this->getNumberOfCrons()." cron jobs");
+		$run = [];
+		$toRun = [];
 		foreach ($keys as $key) {
 			if (isset($this->crons[$key])) {
 				foreach ($this->crons[$key] as $cronjob) {
-					array_push($toRun, $cronjob);
+					$toRun[] = $cronjob;
 				}
 			}
 		}
 
-		if (empty($records)) {
-		    $records = Download::recordIds($this->token, $this->server);
-        }
-
 		register_shutdown_function(["CronManager", "reportCronErrors"]);
 
 		Application::log("Running ".count($toRun)." crons for pid ".$this->pid." with keys ".json_encode($keys));
 		foreach ($toRun as $cronjob) {
+		    $records = $cronjob->getRecords();
+            if (empty($records)) {
+                if (empty($recordsToRun)) {
+                    $records = Download::recordIds($this->token, $this->server);
+                } else {
+                    $records = $recordsToRun;
+                }
+            }
 			Application::log("Running ".$cronjob->getTitle());
 			$run[$cronjob->getTitle()] = array("text" => "Attempted", "ts" => self::getTimestamp());
 			try {
@@ -213,6 +231,15 @@ public function run($passedToken, $passedServer, $passedPid, $records) {
 		}
 	}
 
+	public function setRecords($records) {
+	    $this->records = $records;
+    }
+
+    public function getRecords() {
+	    return $this->records;
+    }
+
 	private $file = "";
 	private $method = "";
+	private $records = [];
 }

classes/EmailManager.php

@@ -136,6 +136,35 @@ private function transformToTS($datetime) {
 		return $ts;
 	}
 
+	public function getQueue($thresholdTs) {
+	    $rows = [];
+        foreach ($this->data as $name => $emailSetting) {
+            foreach ($emailSetting["when"] as $whenType => $datetime) {
+                $ts = self::transformToTS($datetime);
+                if ($ts >= $thresholdTs) {
+                    $processedRows = $this->getRows($emailSetting["who"], $whenType, $this->getForms($emailSetting["what"]));
+                    $emailsByRecord = self::processEmails($processedRows);
+                    $emails = [];
+                    foreach ($emailsByRecord as $recordId => $email) {
+                        if ($email) {
+                            $emails[] = Links::makeRecordHomeLink($this->pid, $recordId, "Record $recordId").": $email";
+                        }
+                    }
+
+                    $row = [];
+                    $row['name'] = $name;
+                    list($row['date'], $row['time']) = explode(" ", $datetime);
+                    $row['from'] = $emailSetting['what']['from'];
+                    $row['subject'] = self::getSubject($emailSetting["what"]);;
+                    $row['to'] = $emails;
+                    $row['to_count'] = count($emails);
+                    $rows[] = $row;
+                }
+            }
+        }
+        return $rows;
+    }
+
 	private function enqueueRelevantEmails($to = "", $names = array(), $func = "sendEmail", $currTime = FALSE) {
 		if (!is_array($names)) {
 			$names = array($names);

classes/Grants.php

@@ -126,7 +126,7 @@ public function getGrants($type = "compiled") {
         if ($type == "all_pis") {
             $grants = $this->dedupedGrants;
             $filteredGrants = [];
-            $piRoles = ["Co-PI", "PI", "Principal Investigator", "Admin", "PI/Co-PI", "Post-doctoral Trainee"];
+            $piRoles = ["Co-PI", "PI", "Principal Investigator", "Admin", "PI/Co-PI"];    // exclude: "Post-Doctoral Trainee"
             foreach ($grants as $grant) {
                 if (in_array($grant->getVariable("role"), $piRoles)) {
                     $filteredGrants[] = $grant;

classes/REDCapManagement.php

@@ -370,7 +370,7 @@ public static function getMaxInstanceForEvent($rows, $eventName, $recordId) {
 
     public static function makeHTMLId($id) {
         $htmlFriendly = preg_replace("/[\s\-]+/", "_", $id);
-        $htmlFriendly = preg_replace("/[\"'#<>\~\`\!\@\#\$\%\^\&\*\(\)\=\;]/", "", $htmlFriendly);
+        $htmlFriendly = preg_replace("/[\+\"\/\[\]'#<>\~\`\!\@\#\$\%\^\&\*\(\)\=\;]/", "", $htmlFriendly);
         return $htmlFriendly;
     }
 

cronLoad.php

@@ -2,6 +2,7 @@
 
 namespace Vanderbilt\FlightTrackerExternalModule;
 
+use Vanderbilt\CareerDevLibrary\Application;
 use \Vanderbilt\CareerDevLibrary\Download;
 use \Vanderbilt\CareerDevLibrary\CronManager;
 
@@ -44,8 +45,14 @@ function loadCrons(&$manager, $specialOnly = FALSE, $token = "", $server = "") {
         $manager->addCron("drivers/13_pullOrcid.php", "pullORCIDs", "Friday");
 		$manager->addCron("publications/getAllPubs_func.php", "getPubs", "Saturday");
 
-        if (date("d") == "18") {
-            $manager->addCron("publications/updateBibliometrics.php", "updateBibliometrics", date("Y-m-d"));
+        # limited group because bibliometric updates take a lot of time due to rate limiters
+		$bibliometricRecordsToUpdate = getRecordsToUpdateBibliometrics($token, $server, date("d"), date("t"));
+		if (!empty($bibliometricRecordsToUpdate)) {
+		    if ((Application::getPid($token) == "112169") && CareerDev::isVanderbilt() && (date("Y-m-d") == "2021-01-23")) {
+                $manager->addCron("publications/updateBibliometrics.php", "updateBibliometrics", date("Y-m-d"));
+            } else {
+                $manager->addCron("publications/updateBibliometrics.php", "updateBibliometrics", date("Y-m-d"), $bibliometricRecordsToUpdate);
+            }
         }
 		$manager->addCron("drivers/6d_makeSummary.php", "makeSummary", "Monday");
 		$manager->addCron("drivers/6d_makeSummary.php", "makeSummary", "Tuesday");
@@ -128,3 +135,13 @@ function checkMetadataForFields($token, $server) {
 	return $vars;
 }
 
+function getRecordsToUpdateBibliometrics($token, $server, $dayOfMonth, $daysInMonth) {
+    $records = Download::recordIds($token, $server);
+    $recordsToRun = [];
+    foreach ($records as $recordId) {
+        if (($recordId - 1) % $daysInMonth == $dayOfMonth - 1) {
+            $recordsToRun[] = $recordId;
+        }
+    }
+    return $recordsToRun;
+}