6.18.0

Application.php

@@ -52,6 +52,19 @@ public static function getRelevantChoices() {
         return CareerDev::getRelevantChoices();
     }
 
+    public static function getJQueryURL(): string {
+        $fileOrder = [
+            APP_PATH_DOCROOT."Resources/webpack/js/bundle.js" => APP_PATH_WEBROOT."Resources/webpack/js/bundle.js",
+            __DIR__."/js/jquery.min.js" => self::link("js/jquery.min.js"),
+        ];
+        foreach ($fileOrder as $file => $url) {
+            if (file_exists($file)) {
+                return $url;
+            }
+        }
+        return "";
+    }
+
     public static function getMetadataFiles($pid): array {
         $files = [];
         if (Application::getSetting("signup_project", $pid)) {
@@ -1168,6 +1181,7 @@ public static function applySecurityHeaders($pid) {
         "citation_title",
         "citation_pub_types",
         "citation_mesh_terms",
+        "citation_pubmed_keywords",
         "citation_journal",
         "citation_volume",
         "citation_issue",

CareerDev.php

@@ -17,7 +17,7 @@ class CareerDev {
 	public static $passedModule = NULL;
 
 	public static function getVersion() {
-		return "6.17.3";
+		return "6.18.0";
 	}
 
     public static function getLocalhostPluginPid() {
@@ -637,6 +637,9 @@ private static function getREDCapSignupURL() {
 
     public static function getLink($relativeUrl, $pid = "", $withWebroot = FALSE) {
         $relativeUrl = preg_replace("/^\//", "", $relativeUrl);
+        if ($relativeUrl == "js/jquery.min.js") {
+            return Application::getJQueryURL();
+        }
         $isMentorAgreementPage = (
             (
                 preg_match("/^mentor\//", $relativeUrl)

autoload.php

@@ -1,6 +1,4 @@
 <?php
 
-namespace Vanderbilt\CareerDevLibrary;
-
-require_once(__DIR__."/../../../redcap_connect.php");
-require_once(__DIR__."/ClassLoader.php");
+require_once(__DIR__."/CareerDev.php");
+require_once(__DIR__."/classes/Autoload.php");

bulkImport.php

@@ -40,11 +40,10 @@
 		$errors = [];
 		list($headers, $lines, $startIdx) = readCSV($_FILES['bulk'], $title);
 
-		$metadata = Download::metadata($token, $server);
-		$records = Download::recordIds($token, $server);
+		$metadata = Download::formMetadata($token, $server, ["position_change", "custom_grant"]);
+		$records = Download::recordIdsByPid($pid);
 		$metadataFields = REDCapManagement::getFieldsFromMetadata($metadata);
 		$choices = REDCapManagement::getChoices($metadata);
-		$matchedIndices = [0];
 		$unmatchedLines = [];
 		$maxInstances = [];
 		$i = 0;
@@ -204,7 +203,7 @@ function verifyFile($fileinfo, $importFile, $expectedItems) {
 	}
 }
 
-function detectFirstError($fileinfo, $importFile, $expected) {
+function detectFirstError(array $fileinfo, string $importFile, int $expected): string {
 	if (!$fileinfo) {
 		return "No file supplied!";
 	}
@@ -221,10 +220,12 @@ function detectFirstError($fileinfo, $importFile, $expected) {
 	$fp = fopen($filename, "r");
     $firstLine = fgetcsv($fp);
 
+    $decrement = 0;
     if ($firstLine[0] == "Record ID") {
         array_shift($headers);
         $headers[0] = "Record ID";
-        $expected--;
+        $decrement = 1;
+        $expected -= $decrement;
     }
 
     # sometimes Excel puts a unicode hidden character before the first element
@@ -254,11 +255,11 @@ function detectFirstError($fileinfo, $importFile, $expected) {
 			return "Line $i has ".count($line)." items! ($expected items expected.)";
 		}
 		if (preg_match("/import\.csv/", $importFile)) {
-            if (!inDateFormat($line[8])) {
-                return "The start date {$line[8]} is not in YYYY-MM-DD or MM-DD-YYYY format!";
+            if (!inDateFormat($line[8 - $decrement])) {
+                return "The start date {$line[8 - $decrement]} is not in YYYY-MM-DD or MM-DD-YYYY format!";
             }
-            if (!inDateFormat($line[9])) {
-                return "The end date {$line[9]} is not in YYYY-MM-DD or MM-DD-YYYY format!";
+            if (!inDateFormat($line[9- $decrement])) {
+                return "The end date {$line[9 - $decrement]} is not in YYYY-MM-DD or MM-DD-YYYY format!";
             }
         }
 		$i++;
@@ -328,7 +329,7 @@ function readCSV($fileinfo, $validationType) {
                 $line[$startIdx + 8] = REDCapManagement::removeMoneyFormatting($line[$startIdx + 8]);
                 $line[$startIdx + 9] = REDCapManagement::removeMoneyFormatting($line[$startIdx + 9]);
             }
-			array_push($lines, $line);
+			$lines[] = $line;
 		}
 		fclose($fp);
 		return [$headers, $lines, $startIdx];
@@ -390,7 +391,7 @@ function getRecordsFromREDCapData($redcapData) {
 	$records = array();
 	foreach ($redcapData as $row) {
 		if (!in_array($row['record_id'], $records)) {
-			array_push($records, $row['record_id']);
+			$records[] = $row['record_id'];
 		}
 	}
 	return $records;

charts/publicationSubjects.php

@@ -48,7 +48,7 @@
         foreach ($fieldsToMonitor as $field) {
             if (isset($row[$field]) && ($row[$field] != "")) {
                 if ($field == OpenAI::CITATION_KEYWORD_FIELD) {
-                    $fieldTerms = OpenAI::explodeKeywords($field);
+                    $fieldTerms = OpenAI::explodeKeywords($row[$field]);
                 } else {
                     $fieldTerms = preg_split("/\s*;\s*/", $row[$field], -1, PREG_SPLIT_NO_EMPTY);
                 }

charts/timeline.php

@@ -23,137 +23,136 @@
 $switches = new FeatureSwitches($token, $server, $pid);
 $switchSettings = $switches->getSwitches();
 
-?>
-
-<?php
-
-	$records = Download::recordIds($token, $server);
-	$recordId = isset($_GET['record']) ? REDCapManagement::getSanitizedRecord($_GET['record'], $records) : $records[0];
-    $nextRecord = $records[0];
-	for ($i = 0; $i < count($records); $i++) {
-		if (($records[$i] == $recordId) && ($i + 1 < count($records))) {
-		    $nextRecord = $records[$i + 1];
-		    break;
-		}
-	}
-    if (isset($redcapData)) {
-        # this page is included via a require_once, so this variable might have already been downloaded
-        $rows = $redcapData;
-    } else {
-        $metadataFields = Download::metadataFields($token, $server);
-        $validPrefixes = [];
-        $grantPrefixes = [
-            "coeus_",
-            "coeussubmission_",
-            "vera_",
-            "verasubmission_",
-            "summary_",
-            "nih_",
-            "reporter_",
-            "custom_",
-        ];
-        $pubPrefixes = [
-            "citation_",
-            "eric_",
-        ];
-        if (($switchSettings["Grants"] != "Off") && !isset($_GET['noCDA'])) {
-            $validPrefixes = array_merge($validPrefixes, $grantPrefixes);
-        }
-        if ($switchSettings["Publications"] != "Off") {
-            $validPrefixes = array_merge($validPrefixes, $pubPrefixes);
-        }
-        $fieldsToDownload = ["record_id", "identifier_first_name", "identifier_middle", "identifier_last_name"];
-        foreach ($validPrefixes as $prefix) {
-            $prefixFields = DataDictionaryManagement::filterFieldsForPrefix($metadataFields, $prefix);
-            $fieldsToDownload = array_unique(array_merge($fieldsToDownload, $prefixFields));
-        }
-        $rows = Download::fieldsForRecords($token, $server, $fieldsToDownload, [$recordId]);
+$records = Download::recordIds($token, $server);
+$recordId = isset($_GET['record']) ? REDCapManagement::getSanitizedRecord($_GET['record'], $records) : $records[0];
+$nextRecord = $records[0];
+for ($i = 0; $i < count($records); $i++) {
+    if (($records[$i] == $recordId) && ($i + 1 < count($records))) {
+        $nextRecord = $records[$i + 1];
+        break;
     }
-
-    $name = "";
-    foreach ($rows as $row) {
-        if ($row['redcap_repeat_instrument'] == "") {
-            $name = $row['identifier_first_name']." ".$row['identifier_last_name'];
-            break;
-        }
+}
+if (isset($redcapData)) {
+    # this page is included via a require_once, so this variable might have already been downloaded
+    $rows = $redcapData;
+} else {
+    $metadataFields = Download::metadataFields($token, $server);
+    $validPrefixes = [];
+    $grantPrefixes = [
+        "coeus_",
+        "coeussubmission_",
+        "vera_",
+        "verasubmission_",
+        "summary_",
+        "nih_",
+        "reporter_",
+        "custom_",
+    ];
+    $pubPrefixes = [
+        "citation_",
+        "eric_",
+    ];
+    if (($switchSettings["Grants"] != "Off") && !isset($_GET['noCDA'])) {
+        $validPrefixes = array_merge($validPrefixes, $grantPrefixes);
     }
+    if ($switchSettings["Publications"] != "Off") {
+        $validPrefixes = array_merge($validPrefixes, $pubPrefixes);
+    }
+    $fieldsToDownload = ["record_id", "identifier_first_name", "identifier_middle", "identifier_last_name"];
+    foreach ($validPrefixes as $prefix) {
+        $prefixFields = DataDictionaryManagement::filterFieldsForPrefix($metadataFields, $prefix);
+        $fieldsToDownload = array_unique(array_merge($fieldsToDownload, $prefixFields));
+    }
+    $rows = Download::fieldsForRecords($token, $server, $fieldsToDownload, [$recordId]);
+}
 
-    $grantsAndPubs = [];
-    $maxTs = [];
-	$minTs = [];
-
-    $grants = new Grants($token, $server, "empty");
-    $grants->setRows($rows);
-    $grants->compileGrants();
-    $grants->compileGrantSubmissions();
-    $id = 1;
-    list($submissions, $submissionTimestamps) = makeSubmissionDots($grants->getGrants("submissions"), $id);
-    if (!empty($submissions) && !isset($_GET['awardsOnly'])) {
-        $classes[] = "AllWithSubmissions";
+$name = "";
+foreach ($rows as $row) {
+    if ($row['redcap_repeat_instrument'] == "") {
+        $name = $row['identifier_first_name']." ".$row['identifier_last_name'];
+        break;
     }
+}
 
-    foreach ($classes as $c) {
-        $maxTs[$c] = 0;
-        $minTs[$c] = time();
-        $grantsAndPubs[$c] = [];
-
-        if ($c == "AllWithSubmissions") {
-            $allTimestamps = $submissionTimestamps;
-            $grantsAndPubs[$c] = $submissions;
-
-            foreach ($allTimestamps as $submissionTs) {
-                if ($submissionTs) {
-                    if ($maxTs[$c] < $submissionTs) {
-                        $maxTs[$c] = $submissionTs;
-                    }
-                    if ($minTs[$c] > $submissionTs) {
-                        $minTs[$c] = $submissionTs;
-                    }
-                }
-            }
-        }
+$grantsAndPubs = [];
+$maxTs = [];
+$minTs = [];
+
+$grants = new Grants($token, $server, "empty");
+$grants->setRows($rows);
+$grants->compileGrants();
+$grants->compileGrantSubmissions();
+$id = 1;
+list($submissions, $submissionTimestamps) = makeSubmissionDots($grants->getGrants("submissions"), $id);
+if (!empty($submissions) && !isset($_GET['awardsOnly'])) {
+    $classes[] = "AllWithSubmissions";
+}
 
-        $grantClass = CareerDev::getSetting("grant_class", $pid);
-        $grantAry = makeTrainingDatesBar($rows, $id, $minTs[$c], $maxTs[$c], ($grantClass == "T"));
-        if ($grantAry) {
-            $grantsAndPubs[$c][] = $grantAry;
-        }
-        if ($switchSettings["Grants"] == "Off") {
-            $grantType = "NONE";
-        } else if (in_array($c, ["All", "AllWithSubmissions"])) {
-            $grantType = "all";
-        } else if (($c == "PubsCDAs") && !isset($_GET['noCDA'])) {
-            $grantType = "prior";
-        } else if (($c == "PubsCDAs") && isset($_GET['noCDA'])) {
-            $grantType = "NONE";
-        } else if ($c == "Flagged") {
-            $grantType = "flagged";
-        } else {
-            throw new \Exception("Class is not set up $c");
-        }
-        if (($grantType !== "NONE") && ($grants->getCount($grantType) > 0)) {
-            if (isset($_GET['test'])) {
-                echo "grants->$grantType has ".$grants->getCount($grantType)." items<br>";
+foreach ($classes as $c) {
+    $maxTs[$c] = 0;
+    $minTs[$c] = time();
+    $grantsAndPubs[$c] = [];
+
+    if ($c == "AllWithSubmissions") {
+        $allTimestamps = $submissionTimestamps;
+        $grantsAndPubs[$c] = $submissions;
+
+        foreach ($allTimestamps as $submissionTs) {
+            if ($submissionTs) {
+                if ($maxTs[$c] < $submissionTs) {
+                    $maxTs[$c] = $submissionTs;
+                }
+                if ($minTs[$c] > $submissionTs) {
+                    $minTs[$c] = $submissionTs;
+                }
             }
-            $grantBars = makeGrantBars($grants->getGrants($grantType), $id, $minTs[$c], $maxTs[$c]);
-            $grantsAndPubs[$c] = array_merge($grantsAndPubs[$c], $grantBars);
         }
+    }
 
-        if (($c == "PubsCDAs") && ($switchSettings["Publications"] != "Off")) {
-            $pubDots = makePubDots($rows, $token, $server, $id, $minTs[$c], $maxTs[$c]);
-            $grantsAndPubs[$c] = array_merge($grantsAndPubs[$c], $pubDots);
+    $grantClass = CareerDev::getSetting("grant_class", $pid);
+    $grantAry = makeTrainingDatesBar($rows, $id, $minTs[$c], $maxTs[$c], ($grantClass == "T"));
+    if ($grantAry) {
+        $grantsAndPubs[$c][] = $grantAry;
+    }
+    if ($switchSettings["Grants"] == "Off") {
+        $grantType = "NONE";
+    } else if (in_array($c, ["All", "AllWithSubmissions"])) {
+        $grantType = "all";
+    } else if (($c == "PubsCDAs") && !isset($_GET['noCDA'])) {
+        $grantType = "prior";
+    } else if (($c == "PubsCDAs") && isset($_GET['noCDA'])) {
+        $grantType = "NONE";
+    } else if ($c == "Flagged") {
+        $grantType = "flagged";
+    } else {
+        throw new \Exception("Class is not set up $c");
+    }
+    if (isset($_GET['test'])) {
+        echo "$c has grantType $grantType and ".$grants->getCount($grantType)." grants<br>";
+    }
+    if (($grantType !== "NONE") && ($grants->getCount($grantType) > 0)) {
+        if (isset($_GET['test'])) {
+            echo "grants->$grantType has ".$grants->getCount($grantType)." items<br>";
         }
+        $grantBars = makeGrantBars($grants->getGrants($grantType), $id, $minTs[$c], $maxTs[$c]);
+        $grantsAndPubs[$c] = array_merge($grantsAndPubs[$c], $grantBars);
+    }
 
-        $currTs = time();
-        if ($maxTs[$c] < $currTs) {
-            $maxTs[$c] = $currTs;
-        }
+    if (($c == "PubsCDAs") && ($switchSettings["Publications"] != "Off")) {
+        $pubDots = makePubDots($rows, $token, $server, $id, $minTs[$c], $maxTs[$c]);
+        $grantsAndPubs[$c] = array_merge($grantsAndPubs[$c], $pubDots);
+    }
 
-        $spacing = ($maxTs[$c] + 90 * 24 * 3600 - $minTs[$c]) / 6;
-        $maxTs[$c] += $spacing;
-        $minTs[$c] -= $spacing;
+    $currTs = time();
+    if ($maxTs[$c] < $currTs) {
+        $maxTs[$c] = $currTs;
     }
 
+    $spacing = ($maxTs[$c] + 90 * 24 * 3600 - $minTs[$c]) / 6;
+    $maxTs[$c] += $spacing;
+    $minTs[$c] -= $spacing;
+}
+
 ?>
     <script src="<?= Application::link("/charts/vis.min.js") ?>"></script>
     <link href="<?= Application::link("charts/vis.min.css") ?>" rel="stylesheet" type="text/css" />