diff --git a/test/run-php-linter.sh b/test/run-php-linter.sh
index d367bb2e8df..a10f21c9b9f 100755
--- a/test/run-php-linter.sh
+++ b/test/run-php-linter.sh
@@ -36,6 +36,7 @@ declare -a tools_list=(
     'raisinbread_refresh.php'
     'recreate_conflicts.php'
     'resetpassword.php'
+    'detect_conflicts.php'
     'setconfig.php'
     'single_use/Cleanup_multiple_firstVisits.php'
     'single_use/Convert_LorisMenuID_to_ModuleID.php'
diff --git a/tools/detect_conflicts.php b/tools/detect_conflicts.php
index 61a81366bc1..74d05dd7c68 100755
--- a/tools/detect_conflicts.php
+++ b/tools/detect_conflicts.php
@@ -1,18 +1,17 @@
 #!/usr/bin/php
 <?php
 /**
- * - Option to detect conflicts for the given instrument 
+ * - Option to detect conflicts for the given instrument
  * and create corresponding CSV file
  * - Option to insert the missing conflict for the given instrument
  * - Option to remove and re-insert conflict for the given instrument
  *
- * PHP version 5
+ * PHP version 7
  *
  * @category Main
- * @package  Loris 
+ * @package  Loris
  * @author   Zia Mohaddes  <zia.mohades@gmail.com>
  * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
- * @license  Loris License
  * @link     https://github.com/aces/Loris
  */
 require_once __DIR__ . "/../vendor/autoload.php";
@@ -25,50 +24,53 @@
 require_once "NDB_Client.class.inc";
 require_once "TimePoint.class.inc";
 
-/* 
- * The minimum number of arguments required to run this script. 
+/*
+ * The minimum number of arguments required to run this script.
  *
- * @var int 
+ * @var int
  */
 const MIN_NUMBER_OF_ARGS = 2;
 
 /*
- * The maximum number of arguments to run this script. 
+ * The maximum number of arguments to run this script.
  *
- * @var int 
+ * @var int
  */
 const MAX_NUMBER_OF_ARGS = 6;
 
 /// User prompt
- 
-if ((count($argv) < MIN_NUMBER_OF_ARGS) || (count($argv) > MAX_NUMBER_OF_ARGS)) {
-
-    echo "Usage: php detect_conflicts.php -i [instrument] -t [timepoint]\n";
-    echo "Example: php detect_conflicts.php -i bdi -t 3month \n\n";
-
-    echo "Usage: php detect_conflicts.php -i [instrument] \n";
-    echo "Example: php detect_conflicts.php -i bdi \n\n";
 
-    echo "Usage: php detect_conflicts.php -r [instrument/all] [-y to confirm]\n";
-    echo "Example: php detect_conflicts.php -r all -y\n";
-    echo "Example: php detect_conflicts.php -r bdi -y \n\n";
-
-    echo "to insert the conflicts into conflicts_unresolved table type -c -i \n";
-    echo "to remove all/re-insert the conflicts into conflicts_unresolved table type -m \n";
-    echo "to run the script for all the instruments simply type -i all \n";
-    echo "to remove ignored conflicts type -r\n\n";
-    echo "NOTE: ONLY THE FAILED VISITS ARE EXCLUDED BY THIS SCRIPT \n";
+if ((count($argv) < MIN_NUMBER_OF_ARGS)
+    || (count($argv) > MAX_NUMBER_OF_ARGS)
+) {
+    echo <<<USAGE
+Usage: php detect_conflicts.php -i [instrument] -t [timepoint]
+Example: php detect_conflicts.php -i bdi -t 3month
+
+Usage: php detect_conflicts.php -i [instrument]
+Example: php detect_conflicts.php -i bdi
+
+Usage: php detect_conflicts.php -r [instrument/all] [-y to confirm]
+Example: php detect_conflicts.php -r all -y
+Example: php detect_conflicts.php -r bdi -y
+
+to insert the conflicts into conflicts_unresolved table type -c -i
+to remove all/re-insert the conflicts into conflicts_unresolved table type -m
+to run the script for all the instruments simply type -i all
+to remove ignored conflicts type -r
+NOTE: ONLY THE FAILED VISITS ARE EXCLUDED BY THIS SCRIPT
+USAGE;
     die();
 }
 
 // parse the options
-$opts = getopt("m:i:t:r:c:y");
-$change = false;
+$opts       = getopt("m:i:t:r:c:y");
+$change     = false;
 $change_all = false;
-$confirm = false;
+$confirm    = false;
 $delete_ignored_conflicts = false;
-$instrument_ignored = null;
-$instrument = null;
+$instrument_ignored       = null;
+$instrument  = null;
 $visit_label = null;
 
 if (!is_array($opts)) {
@@ -89,7 +91,7 @@
 // if ignored but existing conflicts should be included
 if (array_key_exists('r', $opts) && $opts['r'] !=null) {
     $delete_ignored_conflicts = true;
-    $instrument_ignored[0] = $opts['r'];
+    $instrument_ignored[0]    = $opts['r'];
 }
 
 // Set the variables $change and $change_all
@@ -105,23 +107,28 @@
     $confirm = true;
 }
 print_r($opts);
-  
-if (($change && $change_all) || ($delete_ignored_conflicts && ($change || $change_all))) {
-    $die("Choose either Change (-c) or remove and re-insert all conflicts (-m) or remove ignored conflicts (-r)");
+
+if (($change && $change_all)
+    || ($delete_ignored_conflicts && ($change || $change_all))
+) {
+    die(
+        "Choose either Change (-c) or remove and re-insert all conflicts " .
+        "(-m) or remove ignored conflicts (-r)"
+    );
 }
 
 /// Initialization
 $config = NDB_Config::singleton();
-$db = Database::singleton();
+$db     = Database::singleton();
 $ddeInstruments = $config->getSetting('DoubleDataEntryInstruments');
-$db_config = $config->getSetting('database');
-$paths = $config->getSetting('paths');
-$dataDir = $paths['base'] . $config->getSetting('log');
-$diff = null;
-$new_conflicts = array();
-$detected_conflicts = array();
-$current_conflicts = array();
-$conflicts_to_be_excluded = array();
+$db_config      = $config->getSetting('database');
+$paths          = $config->getSetting('paths');
+$dataDir        = $paths['base'] . $config->getSetting('log');
+$diff           = null;
+$new_conflicts  = [];
+$detected_conflicts       = [];
+$current_conflicts        = [];
+$conflicts_to_be_excluded = [];
 
 if ($delete_ignored_conflicts) {
     if ($instrument_ignored[0] == "all") {
@@ -130,49 +137,42 @@
     if (isset($instrument_ignored)) {
         if ($confirm) {
             echo "Removing ignored conflicts\n\n";
-        }
-        else {
+        } else {
             echo "Detecting ignored conflicts\n\n";
         }
         detectIgnoreColumns($instrument_ignored, $confirm);
         if ($confirm) {
             echo "Finished.\n\n";
-        }
-        else {
+        } else {
             echo "\n\nRun this tool again with the argument '-y' to ".
                 "perform the changes\n\n";
         }
     } else {
         echo "No DDE instruments found to remove ignored columns.";
     }
-}
-else {
-
+} else {
     // Check to see if the variable instrument is set
     if (($instrument=='all') ||($instrument=='All')) {
-
         $Factory       = NDB_Factory::singleton();
-        $DB            = $Factory->Database(); //=& Database::singleton();
+        $DB            = $Factory->Database();
         $instruments_q = $DB->pselect(
             "SELECT Test_name FROM test_names",
-            array()
+            []
         );
 
-        $instruments   = array();
+        $instruments = [];
 
         foreach ($instruments_q as $row) {
             if (isset($row['Test_name'])) {
                 $instruments[$row['Test_name']] =$row['Test_name'];
             }
         }
-
     } else {
-        $instruments = array($instrument=>$instrument);
+        $instruments = [$instrument => $instrument];
     }
 
     foreach ($instruments as $instrument) {
         if (isset($instrument)) {
-
             include_once $paths['base'] .
                 "project/instruments/NDB_BVL_Instrument_$instrument.class.inc";
 
@@ -185,18 +185,24 @@
             //check to make sure that the commentids are set
             if (isset($commentids)) {
                 //get the current conflicts
-                $current_conflicts = getCurrentUnresolvedConflicts(
-                    $instrument, $visit_label
+                $current_conflicts  = getCurrentUnresolvedConflicts(
+                    $instrument,
+                    $visit_label
                 );
                 $detected_conflicts = detectConflicts(
-                    $instrument, $commentids, $current_conflicts
+                    $instrument,
+                    $commentids,
+                    $current_conflicts
                 );
 
-                $new_conflicts = getNewConflicts(
-                    $current_conflicts, $detected_conflicts
+                $new_conflicts            = getNewConflicts(
+                    $current_conflicts,
+                    $detected_conflicts
                 );
                 $conflicts_to_be_excluded = detectConflictsTobeExcluded(
-                    $instrument, $commentids, $current_conflicts
+                    $instrument,
+                    $commentids,
+                    $current_conflicts
                 );
                 /**
                  * Only Create report for the  confliclits
@@ -204,34 +210,42 @@
                  * 2) that should be deleted from the conflicts_unresolved table
                  */
                 if ((!$change) && (!$change_all)) {
-
                     //just show the conflicts
                     print "This will only display the conflicts needed to
                 be inserted \n";
                     print "To re-create the conflict, run this script with 
                 -c option \n";
-                    if ((empty($new_conflicts)) && empty($conflicts_to_be_excluded)) {
+                    if ((empty($new_conflicts))
+                        && empty($conflicts_to_be_excluded)
+                    ) {
                         print "No new conflicts or current conflicts to be
                 removed are detected for instrument $instrument \n";
                     } else {
                         writeCSV(
-                            $new_conflicts, $dataDir, $instrument, $visit_label,
+                            $new_conflicts,
+                            $dataDir,
+                            $instrument,
+                            $visit_label,
                             "Conflicts_to_be_inserted"
                         );
                         writeCSV(
-                            $conflicts_to_be_excluded, $dataDir, $instrument,
-                            $visit_label, "Conflicts_to_be_removed"
+                            $conflicts_to_be_excluded,
+                            $dataDir,
+                            $instrument,
+                            $visit_label,
+                            "Conflicts_to_be_removed"
                         );
                     }
                 }
                 /**
-                 * Only insert those conflicts which are new and are not currently
-                 * in the conflict_uresolved
+                 * Only insert those conflicts which are new and are not
+                 * currently in the conflict_uresolved
                  * 1)remove/clear the existing conflicts
                  * 2) And then re-create the conflicts
                  */
 
-                ///if the instrument is not provided, run it only for all the instruments
+                //if the instrument is not provided, run it only for all the
+                //instruments
                 if ($change) {
                     if ((empty($new_conflicts)) || (!isset($new_conflicts))) {
                         die("There are No new conflicts to be inserted ");
@@ -249,22 +263,23 @@
 
 
                 /**
-                 * Remove all the current conflicts for the givent instrument/visit_label
-                 * And re-insert them
+                 * Remove all the current conflicts for the givent
+                 * instrument/visit_label and re-insert them
                  */
                 if ($change_all) {
                     foreach ($commentids as $cid) {
-                        ConflictDetector::clearConflictsForInstance($cid['CommentID']);
+                        ConflictDetector::clearConflictsForInstance(
+                            $cid['CommentID']
+                        );
                         $diff = ConflictDetector::detectConflictsForCommentIds(
-                            $test_name, $cid['CommentID'], $cid['DDECommentID']
+                            $test_name,
+                            $cid['CommentID'],
+                            $cid['DDECommentID']
                         );
                         ConflictDetector::recordUnresolvedConflicts($diff);
                     }
                 }
-
-
             }
-
         } else {
             die("the instrument is not set or there are no commentids \n");
         }
@@ -273,24 +288,23 @@
 
 
 /**
-*Get the commentids for the given instrument, candidate and visit_label
-*
-* @param String $test_name   The instrument been searched
-* @param string $visit_label The  visit_label been searched
-* @param string $candid      The  candid been searched
-* 
-* @return array $commentids An array of commentids found
-*/
-
-function getCommentIDs($test_name, $visit_label=null, $candid=null)
+ * Get the commentids for the given instrument, candidate and visit_label
+ *
+ * @param String  $test_name   The instrument been searched
+ * @param ?string $visit_label The  visit_label been searched
+ * @param ?string $candid      The  candid been searched
+ *
+ * @return array $commentids An array of commentids found
+ */
+function getCommentIDs($test_name, $visit_label = null, $candid = null)
 {
-    $db =& Database::singleton();
-    $params = array();
-    $query = "SELECT CommentID, s.visit_label,Test_name,
+    $db     =& Database::singleton();
+    $params = [];
+    $query  = "SELECT CommentID, s.visit_label,Test_name,
         CONCAT('DDE_', CommentID) AS DDECommentID FROM flag f
         JOIN session s ON (s.ID=f.SessionID)
         JOIN candidate c ON (c.CandID=s.CandID)";
-    $where = " WHERE CommentID NOT LIKE 'DDE%'
+    $where  = " WHERE CommentID NOT LIKE 'DDE%'
         AND s.Active='Y' AND c.Active='Y'
         AND s.Visit <> 'Failure'";
     if ($test_name!=null) {
@@ -298,33 +312,29 @@ function getCommentIDs($test_name, $visit_label=null, $candid=null)
         $params['instrument'] = $test_name;
 
         if (($visit_label!=null) && (isset($visit_label))) {
-            $where .= " AND s.visit_label= :vlabel";
+            $where           .= " AND s.visit_label= :vlabel";
             $params['vlabel'] = $visit_label ;
         }
     }
 
-    $query .=$where;
+    $query     .=$where;
     $commentids = $GLOBALS['DB']->pselect($query, $params);
     return $commentids;
 }
 
-
-
 /**
-*Get the conflicts currently in the conflicts_unresolved table
-*
-* @param String $test_name   The instrument been searched
-* @param string $visit_label The visit_label been searched
-* 
-* @return array $conflicts An array of conflicts detected
-*/
-
-
-function getCurrentUnresolvedConflicts($test_name,$visit_label=null)
+ * Get the conflicts currently in the conflicts_unresolved table
+ *
+ * @param String  $test_name   The instrument been searched
+ * @param ?string $visit_label The visit_label been searched
+ *
+ * @return array $conflicts An array of conflicts detected
+ */
+function getCurrentUnresolvedConflicts($test_name, $visit_label = null): array
 {
-    $db =& Database::singleton();
-    $params = array();
-    $query = "SELECT cu.* FROM conflicts_unresolved cu
+    $db     =& Database::singleton();
+    $params = [];
+    $query  = "SELECT cu.* FROM conflicts_unresolved cu
         JOIN flag f on (f.commentid = cu.commentid1)
         JOIN session s on (s.id = f.sessionid)
         JOIN candidate c on (c.CandID = s.CandID)";
@@ -336,31 +346,29 @@ function getCurrentUnresolvedConflicts($test_name,$visit_label=null)
         $params['instrument'] = $test_name;
 
         if ($visit_label!=null) {
-            $where .= " AND s.visit_label= :visit";
+            $where          .= " AND s.visit_label= :visit";
             $params['visit'] = $visit_label ;
         }
     }
-    $query .=$where;
+    $query    .=$where;
     $conflicts = $db->pselect($query, $params);
     return $conflicts;
 }
 
-
 /**
-* detect the conflicts by 
-* 1) instantiating the instrument for each given commmentid
-* 2) and then taking the diff
-*
-* @param String $test_name         The instrument been searched
-* @param Array  $commentids        An array of commentids used as haystack
-* @param Array  $current_conflicts An array of current conflicts detected
-* 
-* @return Array $detected_conflicts List of newly detected conflicts
-*/
-
-function detectConflicts($test_name,$commentids,$current_conflicts)
+ * Detect the conflicts by
+ * 1) instantiating the instrument for each given commmentid
+ * 2) and then taking the diff
+ *
+ * @param String $test_name         The instrument been searched
+ * @param Array  $commentids        An array of commentids used as haystack
+ * @param Array  $current_conflicts An array of current conflicts detected
+ *
+ * @return Array $detected_conflicts List of newly detected conflicts
+ */
+function detectConflicts($test_name, $commentids, $current_conflicts)
 {
-    $detected_conflicts = array();
+    $detected_conflicts = [];
     /**
      * Go through each commentid
      */
@@ -368,8 +376,10 @@ function detectConflicts($test_name,$commentids,$current_conflicts)
         /**
          * Detect new conflicts
          */
-        $diff=ConflictDetector::detectConflictsForCommentIds(
-            $test_name, $cid['CommentID'], $cid['DDECommentID']
+        $diff =ConflictDetector::detectConflictsForCommentIds(
+            $test_name,
+            $cid['CommentID'],
+            $cid['DDECommentID']
         );
         if ($diff!=null) {
             foreach ($diff as $row) {
@@ -383,18 +393,17 @@ function detectConflicts($test_name,$commentids,$current_conflicts)
 
 
 /**
-*  Write the data into a csv file
-*
-* @param String       $output      Array of data been written into csv
-* @param String $path        The file path
-* @param String $instrument  The name of the instrument
-* @param String $visit_label The name of the visit
-* @param String $prefix      The type of csv file
-* 
-* @return Null
-*/
-
-function writeCSV($output,$path,$instrument,$visit_label,$prefix)
+ *  Write the data into a csv file
+ *
+ * @param String $output      Array of data been written into csv
+ * @param String $path        The file path
+ * @param String $instrument  The name of the instrument
+ * @param String $visit_label The name of the visit
+ * @param String $prefix      The type of csv file
+ *
+ * @return Null
+ */
+function writeCSV($output, $path, $instrument, $visit_label, $prefix)
 {
 
     /**
@@ -415,7 +424,7 @@ function writeCSV($output,$path,$instrument,$visit_label,$prefix)
         unset($column_headers['ExtraKey1']);
         unset($column_headers['ExtraKey2']);
 
-        $column_headers = array_keys($column_headers);
+        $column_headers   = array_keys($column_headers);
         $column_headers[] = "Visit_label";
         $column_headers[] = "PSCID";
         $column_headers[] = "CandID";
@@ -428,8 +437,8 @@ function writeCSV($output,$path,$instrument,$visit_label,$prefix)
             unset($data['ExtraKey2']);
             $info = getInfoUsingCommentID($data['CommentId1']);
             $data['Visit_label'] = $info['Visit_label'];
-            $data['CandID'] = $info['CandID'];
-            $data['PSCID'] = $info['PSCID'];
+            $data['CandID']      = $info['CandID'];
+            $data['PSCID']       = $info['PSCID'];
             fputcsv($fp, $data, "\t"); //write the headers to the CSV file
         }
         fclose($fp);
@@ -441,21 +450,21 @@ function writeCSV($output,$path,$instrument,$visit_label,$prefix)
 
 
 /**
-*  Return data using the commentid
-*
-* @param String $commentid extract data using commentid
-* 
-* @return Array $data        Result of the query
-*/
-
+ * Return data using the commentid
+ *
+ * @param String $commentid extract data using commentid
+ *
+ * @return Array $data        Result of the query
+ */
 function getInfoUsingCommentID($commentid)
 {
-    $db =& Database::singleton();
+    $db   =& Database::singleton();
     $data =  $db->pselectRow(
         "SELECT c.PSCID, c.CandID, s.Visit_label FROM flag f
         JOIN session s on (f.sessionid=s.ID)
         JOIN candidate c on (c.CandID=s.CandID)
-        WHERE f.CommentID = :cid", array('cid'=>$commentid)
+        WHERE f.CommentID = :cid",
+        ['cid' => $commentid]
     );
     return $data;
 }
@@ -463,29 +472,28 @@ function getInfoUsingCommentID($commentid)
 
 
 /**
-* *Detect those conflicts which are currently in the conflicts_unresolved table
-* But should be excluded based on the _doubleDataEntryDiffIgnoreColumns array
-*
-* @param String $instrument        The instrument used for conflict detection
-* @param Array  $commentids        Used for creation of instrument-instantiation
-* @param Array  $current_conflicts An array of current conflicts detected
-* 
-* @return Array $conflicts_to_excluded Array of confllicts to be execluded
-*/
-function detectConflictsTobeExcluded($instrument,$commentids,$current_conflicts)
+ * Detect those conflicts which are currently in the conflicts_unresolved table
+ * But should be excluded based on the _doubleDataEntryDiffIgnoreColumns array
+ *
+ * @param String $instrument        The instrument used for conflict detection
+ * @param Array  $commentids        Used for creation of instrument-instantiation
+ * @param Array  $current_conflicts An array of current conflicts detected
+ *
+ * @return Array $conflicts_to_excluded Array of confllicts to be execluded
+ */
+function detectConflictsTobeExcluded($instrument, $commentids, $current_conflicts)
 {
-
-    $conflicts_to_excluded = array();
-    $instance1 =& NDB_BVL_Instrument::factory(
-        $instrument, $commentids[0]['CommentID'], null
+    $conflicts_to_excluded = [];
+    $instance1      =& NDB_BVL_Instrument::factory(
+        $instrument,
+        $commentids[0]['CommentID'],
+        null
     );
     $ignore_columns = $instance1->_doubleDataEntryDiffIgnoreColumns;
     foreach ($current_conflicts as $conflict) {
-        /**
-         * if the field is part of the ignore_columns, 
-         * and it doesn exist in the conflict array
-         * then track it
-         */
+         // if the field is part of the ignore_columns,
+         // and it doesn exist in the conflict array
+         // then track it
         if (in_array($conflict['FieldName'], $ignore_columns)) {
             $conflicts_to_excluded[] = $conflict;
         }
@@ -493,33 +501,30 @@ function detectConflictsTobeExcluded($instrument,$commentids,$current_conflicts)
     return $conflicts_to_excluded;
 }
 
-
 /**
  * Detect those conflicts not currently in conflicts unresolved table
  *
- * @param Array $current_conflicts   The list of current conflicts detected
+ * @param Array $current_conflicts  The list of current conflicts detected
  * @param Array $detected_conflicts The list of newly created conflicts
- * 
+ *
  * @return Array $new_conflicts  The list of conflicts to be included
  */
-
-function getNewConflicts ($current_conflicts, $detected_conflicts)
+function getNewConflicts($current_conflicts, $detected_conflicts)
 {
-    $new_conflicts = array();
+    $new_conflicts = [];
 
     /**
      * 1) Make sure that the $detected_conflicts is not empty
-     * 2) if the current_conflicts is empty, then the 
+     * 2) if the current_conflicts is empty, then the
      * new conflicts = $detected_conflicts
      */
     if (!(empty($detected_conflicts))) {
         /**
          * 1) go through the current conflicts
-         * 2) and detect those conflicts in recreated conflicts 
+         * 2) and detect those conflicts in recreated conflicts
          * which are not in the current_conflicts
          */
         foreach ($detected_conflicts as $re_conflict) {
-
             if (empty($current_conflicts)) {///if the conflict doesn't exist
                 $new_conflicts[] = $re_conflict;
             } else {
@@ -532,21 +537,20 @@ function getNewConflicts ($current_conflicts, $detected_conflicts)
     return $new_conflicts;
 }
 
-
 /**
- * check to see if the commentid and fieldname exist in the array of conflicts
+ * Check to see if the commentid and fieldname exist in the array of conflicts
  * if it doesn't then return false
  * and if they do, then check to see if the values are the same,
  * if not the same, return false
  *
  * @param String $conflict  The needle
- * @param Array  $conflicts The Haysta
- * 
+ * @param Array  $conflicts The Haystack
+ *
  * @return boolean true if needle exists , else false
  */
-function findConflict($conflict,$conflicts)
+function findConflict($conflict, $conflicts)
 {
-    $found=false;
+    $found =false;
     foreach ($conflicts as $cf) {
         ////////if the value exists then set found to true////
         if ((in_array($conflict['CommentId1'], $cf))
@@ -563,65 +567,82 @@ function findConflict($conflict,$conflicts)
     return false;
 }
 
-
-
-
-
 /**
  * Populates the DDE ignore fields for each instrument and runs
  * the ignoreColumn function on the instrument for the given fields
- * @param $instruments
+ *
+ * @param array $instruments The instruments to check
+ * @param bool  $confirm     Whether to execute
+ *
+ * @return void
+ *
  * @throws Exception
  */
 function detectIgnoreColumns($instruments, $confirm)
 {
-    $instrumentFields = array();
+    $instrumentFields = [];
 
     foreach ($instruments as $instrument) {
         $file = "../project/instruments/NDB_BVL_Instrument_$instrument.class.inc";
         if (file_exists($file)) {
             include_once $file;
-            $commentids = getCommentIDs($instrument, null);
-            $instance =& NDB_BVL_Instrument::factory($instrument, $commentids[0]['CommentID'], null);
+            $commentids      = getCommentIDs($instrument, null);
+            $instance        =& NDB_BVL_Instrument::factory(
+                $instrument,
+                $commentids[0]['CommentID'],
+                null
+            );
             $DDEIgnoreFields = $instance->_doubleDataEntryDiffIgnoreColumns;
 
             if ($DDEIgnoreFields != null) {
                 foreach ($DDEIgnoreFields as $key => $DDEField) {
-                    $instrumentFields = array_merge($instrumentFields, array($DDEField => $instrument));
+                    $instrumentFields = array_merge(
+                        $instrumentFields,
+                        [$DDEField => $instrument]
+                    );
                 }
             } else {
                 echo "No DDE ignore fields found for " . $instrument;
             }
             ignoreColumn($instrument, $instrumentFields, $confirm);
-        }
-        else {
+        } else {
             echo $file . " was not found.\n";
         }
     }
 }
 
 
-/*
+/**
  * Prints the instrument-specific ignore columns to be removed
  * Removes the fields if confirmation is set
+ *
+ * @param string $instrument       The instrument name
+ * @param array  $instrumentFields The instrument fields
+ * @param bool   $confirm          whether to execute the command or not
+ *
+ * @return void
  */
-function ignoreColumn($instrument, $instrumentFields, $confirm) {
+function ignoreColumn($instrument, $instrumentFields, $confirm)
+{
     $db =& Database::singleton();
 
     foreach ($instrumentFields as $field => $instr) {
-
-
-        $query = "SELECT TableName, FieldName, Value1, Value2 FROM conflicts_unresolved 
-          WHERE TableName = '$instrument' AND FieldName = '$field'";
-        $ignoreColumn = $db->pselectOne($query, array());
+        $query        = "SELECT TableName, FieldName, Value1, Value2 
+            FROM conflicts_unresolved 
+            WHERE TableName = '$instrument' AND FieldName = '$field'";
+        $ignoreColumn = $db->pselectOne($query, []);
 
         if (!empty($ignoreColumn)) {
-            $query = "SELECT TableName, FieldName, CommentId1, Value1, CommentId2, Value2 FROM conflicts_unresolved WHERE TableName = '$instrument' AND FieldName = '$field'";
-            $conflictsToRemove = $db->pselect($query, array());
+            $query = "SELECT 
+                TableName, FieldName, CommentId1, Value1, CommentId2, Value2 
+                FROM conflicts_unresolved 
+                WHERE TableName = '$instrument' AND FieldName = '$field'";
+            $conflictsToRemove = $db->pselect($query, []);
             print_r($conflictsToRemove);
 
             if ($confirm) {
-                $query = "DELETE FROM conflicts_unresolved WHERE TableName = '$instrument' AND FieldName = '$field'";
+                $query = "DELETE FROM conflicts_unresolved 
+                    WHERE TableName = '$instrument' AND FieldName = '$field'";
                 $db->run($query);
             }
         }