5.12.9

CareerDev.php

@@ -22,7 +22,7 @@ class CareerDev {
 	public static $passedModule = NULL;
 
 	public static function getVersion() {
-		return "5.12.8";
+		return "5.12.9";
 	}
 
 	public static function getLockFile($pid) {

addNewScholar.php

@@ -39,7 +39,6 @@
         $uploadRow[$field] = REDCapManagement::sanitize($_POST[$field]);
     }
     $feedback = Upload::oneRow($uploadRow, $token, $server);
-    \Vanderbilt\FlightTrackerExternalModule\queueUpInitialEmail($recordId);
     Application::refreshRecordSummary($token, $server, $pid, $recordId);
     if ($feedback['error']) {
         echo "<div class='red padded'>ERROR! " . $feedback['error'] . "</div>\n";

charts/timeline.php

@@ -154,6 +154,7 @@
 	echo "<p style='text-align: center;'><a href='$timelineLink&record=$nextRecord&next'>Next Record</a></p>\n";
 }
 
+$suffix = $pid."_".time();
 foreach ($classes as $c) {
     $divHeader = "";
     $divFooter = "";
@@ -189,8 +190,8 @@
         echo implode("<td>&nbsp;</td>", $cells);
         echo "</tr></tbody></table>";
     }
-    echo "<div id='visualization{$pid}_$c' class='visualization'></div>";
-    echo "<div class='alignright'><button onclick='html2canvas(document.getElementById(\"visualization{$pid}_$c\"), { onrendered: (canvas) => { downloadCanvas(canvas, \"timeline.png\"); } }); return false;' class='smallest'>Save</button></div>";
+    echo "<div id='visualization{$suffix}_$c' class='visualization'></div>";
+    echo "<div class='alignright'><button onclick='html2canvas(document.getElementById(\"visualization{$suffix}_$c\"), { onrendered: (canvas) => { downloadCanvas(canvas, \"timeline.png\"); } }); return false;' class='smallest'>Save</button></div>";
     echo $divFooter;
 }
 
@@ -206,10 +207,10 @@ function runTimeoutToTurnOffEvents(el) {
     }, 2000);
 }
 
-const container_<?= $pid ?> = {};
-const items_<?= $pid ?> = {};
-const options_<?= $pid ?> = {};
-const timeline_<?= $pid ?> = {};
+const container_<?= $suffix ?> = {};
+const items_<?= $suffix ?> = {};
+const options_<?= $suffix ?> = {};
+const timeline_<?= $suffix ?> = {};
 $(document).ready(() => {
     <?php
     foreach ($classes as $c) {
@@ -218,11 +219,11 @@ function runTimeoutToTurnOffEvents(el) {
         $endDate = json_encode(date("Y-m-d", (int) $maxTs[$c]));
 
         echo "
-        container_".$pid."['$c'] = document.getElementById('visualization".$pid."_$c');
-        items_".$pid."['$c'] = new vis.DataSet($dataset);
-        options_".$pid."['$c'] = { start: $startDate, end: $endDate };
+        container_".$suffix."['$c'] = document.getElementById('visualization".$suffix."_$c');
+        items_".$suffix."['$c'] = new vis.DataSet($dataset);
+        options_".$suffix."['$c'] = { start: $startDate, end: $endDate };
         ";
-        echo getJSToLaunchTimeline($pid, $c)."\n";
+        echo getJSToLaunchTimeline($suffix, $c)."\n";
     }
     ?>
 });
@@ -440,10 +441,10 @@ function makePubDots($rows, $token, $server, &$id, &$minTs, &$maxTs) {
     return $grantsAndPubs;
 }
 
-function getJSToLaunchTimeline($pid, $c) {
+function getJSToLaunchTimeline($suffix, $c) {
     $lines = [];
-    $lines[] = "timeline_".$pid."[\"$c\"] = new vis.Timeline(container_".$pid."[\"$c\"], items_".$pid."[\"$c\"], options_".$pid."[\"$c\"]);";
-    $lines[] = "$(timeline_".$pid."[\"$c\"]).unbind(\"mousewheel\");";
-    $lines[] = "runTimeoutToTurnOffEvents(container_".$pid."[\"$c\"]);";
+    $lines[] = "timeline_".$suffix."[\"$c\"] = new vis.Timeline(container_".$suffix."[\"$c\"], items_".$suffix."[\"$c\"], options_".$suffix."[\"$c\"]);";
+    $lines[] = "$(timeline_".$suffix."[\"$c\"]).unbind(\"mousewheel\");";
+    $lines[] = "runTimeoutToTurnOffEvents(container_".$suffix."[\"$c\"]);";
     return implode("", $lines);
 }

classes/DateManagement.php

@@ -166,6 +166,10 @@ public static function REDCapTsToPHPTs($redcapTs) {
         return strtotime("$year-$month-$day");
     }
 
+    public static function PHPTsToREDCapTs($phpTs) {
+        return date("YmdHis", $phpTs);
+    }
+
     public static function getLatestDate($dates) {
         $latestTs = 0;
         $latestDate = "";

classes/ERIC.php

@@ -51,6 +51,9 @@ public static function process($docs, $metadata, $recordId, $listOfPriorIds, $li
                     $prefix."last_update" => date("Y-m-d"),
                     $prefix."link" => "https://eric.ed.gov/?id=$id",
                 ];
+                if (in_array($prefix."created", $ericFields)) {
+                    $uploadRow[$prefix."created"] = date("Y-m-d");
+                }
                 $hasData = FALSE;
                 foreach ($ericFields as $ericField) {
                     $value = $entry[$ericField] ?? "";

classes/Grant.php

@@ -2505,6 +2505,10 @@ private function getCurrentType()
             if (self::getShowDebug()) { Application::log($awardNo.": pi_flag is N"); }
             return "N/A";
         }
+        if (isset($specs['type']) && ($specs['type'] !== "")) {
+            if (self::getShowDebug()) { Application::log($awardNo.": preset type ".$specs['type']); }
+            return $specs['type'];
+        }
 
         if (self::getShowDebug()) { Application::log($awardNo.": First Pass"); }
         if ($type = $this->lexicallyTranslate($awardNo)) {

classes/Grants.php

@@ -10,6 +10,7 @@
 
 class Grants {
     const FLAGGED_GRANTS_SETTING = "flagged_grants";
+    const SPREADSHEET_SOURCES = ["data", "sheet2", "new2017", ];
 
 	public function __construct($token, $server, $metadata = []) {
 		$this->token = $token;
@@ -1562,7 +1563,11 @@ private static function combineGrants($grants) {
 
 					$currEndTs = strtotime($currGrant->getVariable("end"));
 					$grantEndTs = strtotime($basisGrant->getVariable("end"));
-					if ($currEndTs > $grantEndTs) {
+                    if (in_array($basisGrant->getVariable("source"), self::SPREADSHEET_SOURCES)) {
+                        $basisGrant->setVariable("end", self::makeDate($currEndTs));
+                    } else if (in_array($currGrant->getVariable("source"), self::SPREADSHEET_SOURCES)) {
+                        $basisGrant->setVariable("end", self::makeDate($grantEndTs));
+                    } else if ($currEndTs > $grantEndTs) {
 						$basisGrant->setVariable("end", self::makeDate($currEndTs));
 					}
 

classes/PatentsView.php

@@ -114,6 +114,9 @@ public function patents2REDCap($patents, $maxInstance) {
             $row['patent_assignees'] = implode(", ", $assignees["names"]);
             $row['patent_assignee_ids'] = implode(", ", $assignees["ids"]);
             $row['patent_last_update'] = date("Y-m-d");
+            if (in_array("patent_created", $metadataFields)) {
+                $row['patent_created'] = date("Y-m-d");
+            }
             $row['patent_complete'] = "2";
             $rows[] = $row;
         }

classes/Publications.php

@@ -1037,6 +1037,9 @@ private static function xml2REDCap($xml, $recordId, &$instance, $src, $confirmed
             if (in_array("citation_last_update", $metadataFields)) {
                 $row["citation_last_update"] = date("Y-m-d");
             }
+            if (in_array("citation_created", $metadataFields)) {
+                $row["citation_created"] = date("Y-m-d");
+            }
             if (in_array("citation_flagged", $metadataFields)) {
                 $row["citation_flagged"] = "";
             }

classes/RePORTER.php

@@ -284,6 +284,7 @@ private function getNIHUploadRows(&$max, &$existingGrants) {
         $dateFields = ["project_start_date", "project_end_date", "init_encumbrance_date", "award_notice_date",];
         $skip = ["spending_categories", "organization_type", ];
         $upload = [];
+        $metadataFields = Download::metadataFieldsByPid($this->pid);
 
         foreach ($this->getData() as $item) {
             if (!in_array($item['project_num'], $existingGrants)) {
@@ -295,6 +296,9 @@ private function getNIHUploadRows(&$max, &$existingGrants) {
                     "nih_reporter_complete" => "2",
                     "nih_last_update" => date("Y-m-d"),
                 ];
+                if (in_array("nih_created", $metadataFields)) {
+                    $uploadRow["nih_created"] = date("Y-m-d");
+                }
                 foreach ($item as $key => $value) {
                     if (!in_array($key, $skip)) {
                         $newField = "nih_" . strtolower($key);

drivers/19_updateNewCoeus.php

@@ -92,19 +92,23 @@ function updateCoeusGeneric($token, $server, $pid, $records, $instrument, $award
                 Application::log("Record $recordId has ".count($matchedData)." matches for $instrument", $pid);
                 $uniqueFields = [];
                 $timestampField = "";
+                $dateCreatedField = "";
                 if ($instrument == "coeus") {
                     $uniqueFields[] = "coeus_award_no";
                     $uniqueFields[] = "coeus_award_seq";
                     $timestampField = "coeus_update_timestamp";
+                    $dateCreatedField = "coeus_created";
                 } else if ($instrument == "coeus_submission") {
                     $uniqueFields[] = "coeussubmission_ip_number";
                     $uniqueFields[] = "coeussubmission_ip_seq";
                     $timestampField = "coeussubmission_update_timestamp";
+                    $dateCreatedField = "coeussubmission_created";
                 } else {
                     Application::log("No unique fields set => automatically including.", $pid);
                 }
                 $timestampFields = $timestampField ? [$timestampField] : [];
                 $redcapData = Download::fieldsForRecords($token, $server, array_merge(["record_id"], $uniqueFields, $timestampFields), [$recordId]);
+                $dateCreateds = $dateCreatedField ? Download::oneFieldWithInstances($token, $server, $dateCreatedField) : [];
                 $maxInstance = REDCapManagement::getMaxInstance($redcapData, $instrument, $recordId);
                 $uniqueValues = [];
                 foreach ($uniqueFields as $uniqueField) {
@@ -171,13 +175,13 @@ function updateCoeusGeneric($token, $server, $pid, $records, $instrument, $award
                                     )
                                     && !in_array($instance, $uploadInstances)
                                 ) {
-                                    $upload[] = makeUploadRowForCOEUS($dataRow, $recordId, $instrument, $instance, $prefix, $metadataFields);
+                                    $upload[] = makeUploadRowForCOEUS($dataRow, $recordId, $instrument, $instance, $prefix, $metadataFields, $dateCreateds);
                                 }
                             }
                         }
                     } else {
                         $maxInstance++;
-                        $upload[] = makeUploadRowForCOEUS($dataRow, $recordId, $instrument, $maxInstance, $prefix, $metadataFields);
+                        $upload[] = makeUploadRowForCOEUS($dataRow, $recordId, $instrument, $maxInstance, $prefix, $metadataFields, $dateCreateds);
                     }
                 }
                 if (!empty($upload)) {
@@ -250,14 +254,18 @@ function dedupCOEUS($token, $server, $pid, $recordId, $instrument, $prefix, $uni
     }
 }
 
-function makeUploadRowForCOEUS($dataRow, $recordId, $instrument, $instance, $prefix, $metadataFields) {
+function makeUploadRowForCOEUS($dataRow, $recordId, $instrument, $instance, $prefix, $metadataFields, $dateCreateds) {
     $uploadRow = [
         "record_id" => $recordId,
         "redcap_repeat_instrument" => $instrument,
         "redcap_repeat_instance" => $instance,
         $prefix."last_update" => date("Y-m-d"),
         $instrument."_complete" => "2",
     ];
+    $dateCreated = $dateCreateds[$recordId][$instance] ?? "";
+    if (!$dateCreated) {
+        $uploadRow[$prefix."created"] = date("Y-m-d");
+    }
     foreach ($dataRow as $dataField => $value) {
         if ($value) {
             $field = $prefix.strtolower($dataField);

drivers/20_nsf.php

@@ -183,6 +183,7 @@ function transformIntoREDCap($recordMatches, $token, $server) {
 
     $errors = [];
     $totalAwards = 0;
+    $metadataFields = Download::metadataFields($token, $server);
     foreach ($recordMatches as $recordId => $awards) {
         if (!empty($awards)) {
             $totalAwards += count($awards);
@@ -198,6 +199,9 @@ function transformIntoREDCap($recordMatches, $token, $server) {
                         "nsf_last_update" => date("Y-m-d"),
                         $instrument."_complete" => "2",
                     ];
+                    if (in_array("nsf_created", $metadataFields)) {
+                        $uploadRow["nsf_created"] = date("Y-m-d");
+                    }
                     foreach ($fields as $field) {
                         if (!isset($award[$field])) {
                             continue;

drivers/24_getIES.php

@@ -92,6 +92,9 @@ function matchNamesWithExcel($excelData, $token, $server, $pid) {
                         "redcap_repeat_instance" => $maxInstance[$recordId] + 1,
                         "ies_grant_complete" => "2",
                     ];
+                    if (in_array("ies_created", $metadataFields)) {
+                        $uploadRow["ies_created"] = date("Y-m-d");
+                    }
                     $originalCount = count($uploadRow);
                     makeREDCapForIES($uploadRow, $spreadsheet->getActiveSheet(), $headerRow, $rowNum, $prefix, $metadataFields);
                     if (

drivers/25_emailHighlights.php

@@ -51,14 +51,20 @@ function sendEmailHighlights($token, $server, $pid, $records, $allPids = FALSE)
     $pmidsIdentified = [];
     $pidsCitationRecordsAndInstances = [];
     $pidsGrantRecordsAndInstances = [];
-    $fields = ["record_id", "citation_authors", "citation_pmid", "citation_ts", "citation_include", "citation_rcr", "citation_altmetric_score", "coeus_last_update", "nih_last_update", "vera_last_update"];
+    $fields = ["record_id", "citation_authors", "citation_pmid", "citation_ts", "citation_include", "citation_rcr", "citation_altmetric_score",];
     $grantInstrumentsAndPrefices = [
         "nih_reporter" => "nih",
         "nsf" => "nsf",
         "coeus" => "coeus",
         "vera" => "vera",
         "custom_grant" => "custom",
+        "ies_grant" => "ies",
     ];
+    foreach(array_values($grantInstrumentsAndPrefices) as $prefix) {
+        $fields[] = $prefix."_last_update";
+        $fields[] = $prefix."_created";
+    }
+    $fields = array_unique($fields);
     $names = [];
     $emails = [];
     $allMetadata = [];
@@ -142,9 +148,17 @@ function sendEmailHighlights($token, $server, $pid, $records, $allPids = FALSE)
                         $prefix = $grantInstrumentsAndPrefices[$instrument];
                         $instance = $row['redcap_repeat_instance'];
                         $lastUpdate = $row[$prefix.'_last_update'];
+                        $dateCreated = $row[$prefix.'_created'] ?? "";
                         if (
-                            $lastUpdate
-                            && (strtotime($lastUpdate) > $warningTs)
+                            (
+                                $dateCreated
+                                && (strtotime($dateCreated) > $warningTs)
+                            )
+                            || (
+                                !$dateCreated
+                                && $lastUpdate
+                                && (strtotime($lastUpdate) > $warningTs)
+                            )
                         ) {
                             enrollNewInstance($pidsGrantRecordsAndInstances, $currPid, $recordId, $instance, $instrument);
                         }
@@ -294,7 +308,7 @@ function sendEmailHighlights($token, $server, $pid, $records, $allPids = FALSE)
     for ($i = 0; $i < count($requestedGrants); $i++) {
         $requestedGrants[$i] = Grant::translateToBaseAwardNumber($requestedGrants[$i]);
     }
-    $htmlRows = ["<h2>Publications After $thresholdDate</h2>"];
+    $htmlRows = ["<h2>All Publications After $thresholdDate</h2>"];
     $performanceRows = ["<h2>Publications With Newly Altmetric &gt; " . Altmetric::THRESHOLD_SCORE . " or RCR &gt; " . iCite::THRESHOLD_SCORE . "</h2>"];
     $publicationPids = array_unique(array_merge(array_keys($scholarsIdentified), array_keys($pidsCitationRecordsAndInstances)));
     if (!empty($publicationPids)) {
@@ -705,4 +719,4 @@ function filterForInstitution(&$records, $token, $server, $pid, $metadata) {
         }
     }
     $records = $filteredRecords;
-}
+}