5.8.0

vanderbilt-redcap · Jun 9, 2023 · 732f538 · 732f538
1 parent 1da4449
commit 732f538
Show file tree

Hide file tree

Showing 17 changed files with 264 additions and 165 deletions.
diff --git a/Application.php b/Application.php
@@ -293,8 +293,8 @@ public static function log($mssg, $pid = FALSE) {
 		CareerDev::log($mssg, $pid);
 	}
 
-	public static function getInstitutions($pid = NULL) {
-		return CareerDev::getInstitutions($pid);
+	public static function getInstitutions($pid = NULL, $searchOnly = TRUE) {
+		return CareerDev::getInstitutions($pid, $searchOnly);
 	}
 
 	public static function getImportHTML() {
@@ -325,10 +325,10 @@ public static function getImportHTML() {
         return $str;
     }
 
-	public static function getHeader($tokenName = "") {
-        $pid = CareerDev::getPID();
-        $token = self::getSetting("token", $pid);
-        $server = self::getSetting("server", $pid);
+	public static function getHeader($tokenName = "", $token = "", $server = "", $pid = "") {
+        $pid = $pid ?: CareerDev::getPID();
+        $token = $token ?: self::getSetting("token", $pid);
+        $server = $server?: self::getSetting("server", $pid);
 
         if (!$tokenName) {
             $tokenName = self::getSetting("tokenName", $pid);
@@ -412,22 +412,22 @@ public static function getHeader($tokenName = "") {
 
         $navBar = new NavigationBar();
         $navBar->addFALink("home", "Home", CareerDev::getHomeLink());
-        $navBar->addFAMenu("clinic-medical", "General", CareerDev::getMenu("General"));
+        $navBar->addFAMenu("clinic-medical", "General", CareerDev::getMenu("General", $pid));
         if ($switches->isOnForProject("Grants")) {
             $navBar->addMenu("<img src='".CareerDev::link("/img/grant_small.png")."'>Grants", CareerDev::getMenu("Grants"));
         }
         if ($switches->isOnForProject("Publications")) {
-            $navBar->addFAMenu("sticky-note", "Pubs", CareerDev::getMenu("Pubs"));
+            $navBar->addFAMenu("sticky-note", "Pubs", CareerDev::getMenu("Pubs", $pid));
         }
-        $navBar->addFAMenu("table", "View", CareerDev::getMenu("View"));
-        $navBar->addFAMenu("calculator", "Wrangle", CareerDev::getMenu("Wrangler"));
-        $navBar->addFAMenu("school", "Scholars", CareerDev::getMenu("Scholars"));
-        $navBar->addMenu("<img src='".CareerDev::link("/img/redcap_translucent_small.png")."'>REDCap", CareerDev::getMenu("REDCap"));
-        $navBar->addFAMenu("tachometer-alt", "Dashboards", CareerDev::getMenu("Dashboards"));
-        $navBar->addFAMenu("filter", "Cohorts / Filters", CareerDev::getMenu("Cohorts"));
-        $navBar->addFAMenu("chalkboard-teacher", "Mentors", CareerDev::getMenu("Mentors"));
-        $navBar->addFAMenu("pen", "Resources", CareerDev::getMenu("Resources"));
-        $navBar->addFAMenu("question-circle", "Help", CareerDev::getMenu("Help"));
+        $navBar->addFAMenu("table", "View", CareerDev::getMenu("View", $pid));
+        $navBar->addFAMenu("calculator", "Wrangle", CareerDev::getMenu("Wrangler", $pid));
+        $navBar->addFAMenu("school", "Scholars", CareerDev::getMenu("Scholars", $pid));
+        $navBar->addMenu("<img src='".CareerDev::link("/img/redcap_translucent_small.png")."'>REDCap", CareerDev::getMenu("REDCap", $pid));
+        $navBar->addFAMenu("tachometer-alt", "Dashboards", CareerDev::getMenu("Dashboards", $pid));
+        $navBar->addFAMenu("filter", "Cohorts / Filters", CareerDev::getMenu("Cohorts", $pid));
+        $navBar->addFAMenu("chalkboard-teacher", "Mentors", CareerDev::getMenu("Mentors", $pid));
+        $navBar->addFAMenu("pen", "Resources", CareerDev::getMenu("Resources", $pid));
+        $navBar->addFAMenu("question-circle", "Help", CareerDev::getMenu("Help", $pid));
         $str .= $navBar->getHTML();
 
         return $str;
@@ -549,11 +549,14 @@ public static function getPids() {
             } else if (self::isServer("redcaptest.vanderbilt.edu")) {
                 # TODO Add test projects with plugin
             }
-            return $pids;
         } else {
             $module = self::getModule();
-            return $module->getPids();
+            $pids = $module->getPids();
         }
+        for ($i = 0; $i < count($pids); $i++) {
+            $pids[$i] = (string) $pids[$i];
+        }
+        return $pids;
     }
 
     public static function getActiveSourcePids() {

diff --git a/CareerDev.php b/CareerDev.php
@@ -22,7 +22,7 @@ class CareerDev {
 	public static $passedModule = NULL;
 
 	public static function getVersion() {
-		return "5.7.18";
+		return "5.8.0";
 	}
 
 	public static function getLockFile($pid) {
@@ -596,32 +596,41 @@ public static function getInstitutionCount() {
 		return count(self::getInstitutions());
 	}
 
-	public static function getInstitutions($pid = NULL) {
-		$shortInst = self::getShortInstitution($pid);
-		$longInst = self::getInstitution($pid);
+	public static function getInstitutions($pid = NULL, $searchOnly = TRUE) {
+        if ($searchOnly) {
+            $shortInst = self::getShortInstitution($pid);
+            $longInst = self::getInstitution($pid);
 
-		$institutions = array();
-		if (preg_match("/".strtolower($shortInst)."/", strtolower($longInst))) {
-			$institutions[] = $shortInst;
-			$institutions[] = $longInst;
-		} else {
-			$institutions[] = $longInst;
-		}
+            $institutions = array();
+            if (preg_match("/".strtolower($shortInst)."/", strtolower($longInst))) {
+                $institutions[] = $shortInst;
+                $institutions[] = $longInst;
+            } else {
+                $institutions[] = $longInst;
+            }
 
-		$otherInsts = preg_split("/\s*[,\/]\s*/", self::getSetting("other_institutions", $pid));
-		foreach ($otherInsts as $otherInst) {
-			if ($otherInst && !in_array($otherInst, $institutions)) {
-				$institutions[] = $otherInst;
-			}
-		}
-        foreach ($institutions as $i => $institution) {
-            $institutions[$i] = str_replace("&#039;", "'", $institution);
-            $institutions[$i] = str_replace("&#39;", "'", $institutions[$i]);
-            $institutions[$i] = str_replace("&amp;", "&", $institutions[$i]);
-            $institutions[$i] = str_replace("&quot;", "\"", $institutions[$i]);
-        }
+            $otherInsts = preg_split("/\s*[,\/]\s*/", self::getSetting("other_institutions", $pid));
+            foreach ($otherInsts as $otherInst) {
+                if ($otherInst && !in_array($otherInst, $institutions)) {
+                    $institutions[] = $otherInst;
+                }
+            }
+            foreach ($institutions as $i => $institution) {
+                $institutions[$i] = str_replace("&#039;", "'", $institution);
+                $institutions[$i] = str_replace("&#39;", "'", $institutions[$i]);
+                $institutions[$i] = str_replace("&amp;", "&", $institutions[$i]);
+                $institutions[$i] = str_replace("&quot;", "\"", $institutions[$i]);
+            }
 
-		return $institutions;
+            return $institutions;
+        } else {
+            $displayInstitutionList = self::getSetting("display_institutions", $pid);
+            if (!$displayInstitutionList) {
+                return self::getInstitutions($pid, TRUE);
+            } else {
+                return preg_split("/\s*[,;]\s*/", trim($displayInstitutionList));
+            }
+        }
 	}
 
 	public static function isEligible($pid) {
@@ -821,8 +830,10 @@ public static function getSetting($field, $pid = "") {
             }
             if (file_exists(self::getCredentialsFile())) {
                 include(self::getCredentialsFile());
-                if (isset($info['prod'][$field])) {
+                if (isset($info['prod'][$field]) && ($pid == NEWMAN_SOCIETY_PROJECT)) {
                     return $info['prod'][$field];
+                } else if (isset($info['localhost'][$field]) && ($pid == LOCALHOST_TEST_PROJECT)) {
+                    return $info['localhost'][$field];
                 }
             }
             if (($field == "admin_email") || ($field == "adminEmail")) {
@@ -1036,8 +1047,8 @@ public static function has($instrument, $pid = "") {
         return FALSE;
     }
 
-	public static function getMenu($menuName) {
-		$pid = self::getPid();
+	public static function getMenu($menuName, $pid = NULL) {
+		$pid = $pid ?: self::getPid();
 		$r = self::getREDCapDir();
         if ($menuName == "Grants") {
             $ary = [
@@ -1080,7 +1091,7 @@ public static function getMenu($menuName) {
                 "REDCap Reports" => $r."/DataExport/index.php",
                 "Missingness Report<br>(Computationally Expensive)" => self::link("/tablesAndLists/missingness.php"),
             ];
-            if (self::has("patent") && $switches->isOnForProject("Patents")) {
+            if (self::has("patent", $pid) && $switches->isOnForProject("Patents")) {
                 $ary["Patent Viewer"] = self::link("patents/view.php");
             }
             return $ary;
@@ -1090,7 +1101,7 @@ public static function getMenu($menuName) {
             $server = self::getSetting("server", $pid);
             $switches = new FeatureSwitches($token, $server, $pid);
 		    $ary = [];
-		    if (self::has("mentoring_agreement") && $switches->isOnForProject("Mentee-Mentor")) {
+		    if (self::has("mentoring_agreement", $pid) && $switches->isOnForProject("Mentee-Mentor")) {
                 $ary["Configure Mentee-Mentor Agreements"] = self::link("/mentor/config.php");
                 $ary["Add Mentors for Existing Scholars"] = self::link("addMentor.php");
                 $ary["Mentee-Mentor Agreements Dashboard"] = self::link("/mentor/dashboard.php");
@@ -1133,7 +1144,7 @@ public static function getMenu($menuName) {
 					"Dates" => self::link("/dashboard/dates.php"),
 					"Resources" => self::link("/dashboard/resources.php"),
 					];
-			if (self::has("mentoring_agreement")) {
+			if (self::has("mentoring_agreement", $pid)) {
 			    $ary["Mentee-Mentor Agreements"] = self::link("mentor/dashboard.php");
             }
             return $ary;
@@ -1226,7 +1237,7 @@ public static function getMenu($menuName) {
                 $ary["Lexical Translator"] = self::link("/lexicalTranslator.php");
             }
             $ary["Position Change Wrangler"] = self::link("/wrangler/positions.php");
-			if (self::has("patent") && $switches->isOnForProject("Patents")) {
+			if (self::has("patent", $pid) && $switches->isOnForProject("Patents")) {
                 $ary["Patent Wrangler"] = self::link("/wrangler/include.php")."&wranglerType=Patents";
             }
 			return $ary;

diff --git a/FlightTrackerExternalModule.php b/FlightTrackerExternalModule.php
@@ -1009,7 +1009,11 @@ function redcap_every_page_before_render($project_id) {
             echo "<script src='".CareerDev::link("/js/jquery.min.js")."'></script>\n";
             echo "
 <script>
-    $(document).ready(function() { $('.chklist.round:eq(6)').hide(); });
+    $(document).ready(function() {
+        $('.chklist.round:eq(6)')
+            .hide()
+            .after('<p>By design, Flight Tracker projects should not move to production status because they need to update their Data Dictionaries without manual review. This must be done in development mode. Therefore, moving to production is disabled.</p>')
+    });
 </script>\n";
         } else if (PAGE == "DataEntry/index.php") {
             echo "<script src='".CareerDev::link("/js/jquery.min.js")."'></script>\n";
@@ -1156,7 +1160,7 @@ function hasMentorAgreementRights($project_id, $userid)
 
     function makeHeaders($token, $server, $pid, $tokenName) {
 	    $str = "";
-	    $str .= Application::getHeader($tokenName);
+	    $str .= Application::getHeader($tokenName, $token, $server, $pid);
         if (!CareerDev::isFAQ() && CareerDev::isHelpOn()) {
             $currPage = CareerDev::getCurrPage();
             $str .= "<script>$(document).ready(function() { showHelp('".CareerDev::getHelpLink()."', '".$currPage."'); });</script>";

diff --git a/add.php b/add.php
@@ -19,7 +19,7 @@
     list($lines, $matchedMentorUids, $newMentorNames) = parsePostForLines($_POST);
     $newLines = [];
     $originalMentorNames = [];
-    if (!empty($matchedMentorUids)) {
+    if (!empty($matchedMentorUids) || Application::isLocalhost()) {
         $mentorCol = 13;
         for ($i = 0; $i < count($lines); $i++) {
             if (isset($newMentorNames[$i])) {
@@ -35,7 +35,7 @@
             }
         }
         $newUids = getUidsForMentors($newLines);
-        if (!empty($newUids)) {
+        if (!empty($newUids) || Application::isLocalhost()) {
             echo makeAdjudicationTable($lines, $newUids, $matchedMentorUids, $originalMentorNames);
         } else {
             commitChanges($token, $server, $lines, $matchedMentorUids, $pid, $createRecordsURI);
@@ -87,7 +87,7 @@
         throw new \Exception("This should never happen.");
     }
 	$mentorUids = getUidsForMentors($lines);
-	if (!empty($mentorUids)) {
+	if (!empty($mentorUids) || Application::isLocalhost()) {
         echo makeAdjudicationTable($lines, $mentorUids, [], []);
         $url = APP_PATH_WEBROOT."ProjectGeneral/keep_alive.php?pid=".$pid;
         echo "<script>
@@ -501,7 +501,7 @@ function makeAdjudicationTable($lines, $mentorUids, $existingUids, $originalMent
     $html .= "<script>
 $(document).ready(() => {
     if ($('.mentorKeep').length > 0) {
-        $('form#mainForm').prepend('<p class=\"centered\"><button onclick=\"checkAllMentors(); return false;\">Check All for Uploading Unmatched Mentors</button></p>');
+        $('form#mainForm').prepend('<p class=\"centered\"><button class=\"green\" onclick=\"checkAllMentors(); return false;\">Check All for Uploading Unmatched Mentors</button></p>');
     }
 });
 
@@ -527,7 +527,7 @@ function processMentorName($currMentorName, $currMentorUids, $i, $customLine, $c
         $hiddenField = "<input type='hidden' name='originalmentorname___$i' value='$escapedMentorName'>";
         $mentorKeep = "mentorkeep___$i";
         $html .= "<td class='red'>";
-        $html .= "<strong>No names in REDCap matched with $currMentorName.</strong><br>Keep mentor? <input type='radio' class='mentorKeep' name='$mentorKeep' id='$mentorKeep' value='1'> <label for='$mentorKeep'> Yes, upload anyways</label><br>Or perhaps there is a nickname and/or a maiden name at play here. Do you want to try adjusting their name?<br>$hiddenField<input type='text' name='newmentorname___$i' value='$escapedMentorName'><br>";
+        $html .= "<strong>No names in REDCap matched with $currMentorName.</strong><br>Keep mentor? <input type='radio' class='mentorKeep' name='$mentorKeep' id='$mentorKeep' value='1' /> <label for='$mentorKeep'> Yes, upload anyways</label><br>Or perhaps there is a nickname and/or a maiden name at play here. Do you want to try adjusting their name?<br>$hiddenField<input type='text' name='newmentorname___$i' value='$escapedMentorName'><br>";
         $html .= "<br>Or try a custom id?<br>".$customLine.$customHidden;
         $html .= "</td>";
     } else if (count($currMentorUids) == 1) {

diff --git a/charts/baseWeb.php b/charts/baseWeb.php
@@ -51,16 +51,17 @@ function goToUrl(url) {
 		}
 	</script>";
 }
+if (!isset($_GET['hideHeader'])) {
 
 ?>
 <!DOCTYPE html>
 <title>Flight Tracker for Scholars</title>
 <?php
-if (!isset($_GET['headers']) || ($_GET['headers'] != "false")) {
-    echo makeHeaders(Application::getModule(), $token, $server, $pid, $tokenName);
-} else {
-    echo Application::getImportHTML();
-}
+    if (!isset($_GET['headers']) || ($_GET['headers'] != "false")) {
+        echo makeHeaders(Application::getModule(), $token, $server, $pid, $tokenName);
+    } else {
+        echo Application::getImportHTML();
+    }
 
 ?>
 <?= CareerDev::makeBackgroundCSSLink() ?>
@@ -155,4 +156,8 @@ function search(page, div, name) {
 	}
 }
 
-</script>
+</script>
+
+<?php
+
+}
diff --git a/classes/Consortium.php b/classes/Consortium.php
@@ -14,12 +14,13 @@ public static function findNextMeeting($startTime = NULL) {
 	}
 
 	public static function findNextMeetingTs($startTime = NULL, $weekNum = 1) {
-        	$meetTwiceAMonth = FALSE;
 		if (!$startTime) {
 			if (date("Y-m") == "2020-02") {
-				# start twice a month in 2020-03
-				$startTime = strtotime("2020-03-01");
-			} else {
+                # start twice a month in 2020-03
+                $startTime = strtotime("2020-03-01");
+            } else if (in_array(date("Y-m"), ["2023-06", "2023-07"]) && ($weekNum == 1)) {
+                $startTime = strtotime("2023-08-01");
+            } else {
 				$startTime = time();
 			}
 		}

diff --git a/classes/DataDictionaryManagement.php b/classes/DataDictionaryManagement.php
@@ -257,13 +257,7 @@ public static function installMetadataFromFiles($files, $token, $server, $pid, $
             }
         }
         if (!empty($metadata['file'])) {
-            if ($grantClass == "K") {
-                $mentorLabel = "Primary mentor during your K/K12 training period";
-            } else if ($grantClass == "T") {
-                $mentorLabel = "Primary mentor during your pre-doc/post-doc training period";
-            } else {
-                $mentorLabel = "Primary mentor (current)";
-            }
+            $mentorLabel = "Primary mentor during your training period";
             $fieldLabels = [];
             foreach ($metadata as $type => $md) {
                 $fieldLabels[$type] = self::getLabels($md);
@@ -1067,7 +1061,7 @@ private static function alterOptionalFields(&$metadata, $pid) {
 
     private static function alterInstitutionFields(&$metadata, $pid) {
         if ($pid) {
-            $institutions = Application::getInstitutions();
+            $institutions = Application::getInstitutions($pid, FALSE);
             if (empty($institutions)) {
                 $institutions = ["Home Institution"];
             }

diff --git a/classes/NameMatcher.php b/classes/NameMatcher.php
@@ -873,7 +873,11 @@ public static function splitName($name, $parts = 2, $loggingOn = FALSE, $clearOf
                 }
             }
 		}
-		return array("", "");
+        $ary = [];
+        for ($i = 0; $i < $parts; $i++) {
+            $ary[] = "";
+        }
+        return $ary;
 	}
 
 	public static function clearOfHonorifics($nodes) {