[Imaging browser] Fix loading error for t1-defaced and t2-defaced sca…

…n types (#6668)

Adding 't1-defaced' or 't2-defaced' scan types to the imaging browser was causing an SQL error due to the hyphen in the name. Escape (or quote as necessary) the references to the scan type in the SQL query.

    Resolves #6616

modules/imaging_browser/php/imagingbrowserrowprovisioner.class.inc

@@ -33,10 +33,13 @@ class ImagingBrowserRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisi
     /**
      * Create an ImagingBrowserRowProvisioner, which gets rows for
      * the imaging browser menu table.
+     *
+     * @throws \ConfigurationException
      */
     function __construct()
     {
         $config = \NDB_Config::singleton();
+        $DB     = \NDB_Factory::singleton()->database();
 
         // ===========================================================
         // Get the different scan types to be displayed in data table
@@ -92,7 +95,7 @@ class ImagingBrowserRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisi
         }
 
         $NewDataSubquery = "
-            CASE 
+            CASE
                 COALESCE(Max(fqc.QCLastChangeTime), 'new')
                 WHEN 'new' THEN {$acqpif}
                 WHEN ''    THEN {$acqpif}
@@ -109,9 +112,9 @@ class ImagingBrowserRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisi
         $coalesce_desc = array();
 
         foreach ($scan_id_types as $id => $type) {
-            $pass[$id]          = $type . 'pass';
-            $qc[$id]            = $type . 'QC';
-            $coalesce_desc[$id] = $pass[$id] . '.' . $qc[$id];
+            $pass[$id]          = $DB->escape($type);
+            $qc[$id]            = $DB->quote($type);
+            $coalesce_desc[$id] = $DB->quote($pass[$id] . '.' . $qc[$id]);
             $case_desc[$id]     = "
                 CASE
                     COALESCE($coalesce_desc[$id], '')
@@ -126,15 +129,15 @@ class ImagingBrowserRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisi
                 WHEN 'Fail' THEN
                     IF(s.MRIQCPending='Y', 'Pending Fail', 'Fail')
                 WHEN 'Pass' THEN
-                    IF(s.MRIQCPending='Y', 'Pending Pass', 'Pass') 
+                    IF(s.MRIQCPending='Y', 'Pending Pass', 'Pass')
                 ELSE s.MRIQCStatus
-            END 
+            END
             ";
 
         $PendingNewquery = "
-            CASE 
+            CASE
                 WHEN s.MRIQCPending='Y' THEN 'P'
-                WHEN MAX(fqc.QCFirstChangeTime) IS NULL $newQueryCase THEN  'N'      
+                WHEN MAX(fqc.QCFirstChangeTime) IS NULL $newQueryCase THEN  'N'
             END";
 
         // ====================================================
@@ -146,13 +149,13 @@ class ImagingBrowserRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisi
         foreach ($case_desc as $key => $value) {
             $left_joins .= "
             LEFT JOIN (
-              SELECT files.SessionID, 
-                MIN(files_qcstatus.QCStatus+0) as $qc[$key] 
-              FROM files 
-              JOIN files_qcstatus USING (FileID) 
-              WHERE files.AcquisitionProtocolID= $key 
-                AND files_qcstatus.QCStatus IN (1, 2) 
-              GROUP BY files.SessionID) $pass[$key] 
+              SELECT files.SessionID,
+                MIN(files_qcstatus.QCStatus+0) as $qc[$key]
+              FROM files
+              JOIN files_qcstatus USING (FileID)
+              WHERE files.AcquisitionProtocolID= $key
+                AND files_qcstatus.QCStatus IN (1, 2)
+              GROUP BY files.SessionID) $pass[$key]
                 ON ($pass[$key].SessionID=f.SessionID
             ) ";
         }
@@ -166,15 +169,16 @@ class ImagingBrowserRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisi
         // $scan_types are set in the configuration module
         $modalities_subquery = '';
         foreach ($case_desc as $key => $value) {
-            $modalities_subquery = "$value as $scan_id_types[$key]_QC_Status";
+            $modalities_subquery = $value." as " .
+                $DB->quote("$scan_id_types[$key]_QC_Status");
         }
 
         // =================================================
         // Final query
         // =================================================
 
         parent::__construct(
-            "SELECT 
+            "SELECT
               p.Name as Site,
               c.PSCID as PSCID,
               c.CandID as DCCID,
@@ -189,22 +193,22 @@ class ImagingBrowserRowProvisioner extends \LORIS\Data\Provisioners\DBRowProvisi
               s.ID as sessionID,
               GROUP_CONCAT(DISTINCT modality.Scan_type) as sequenceType,
               $PendingNewquery as pending," .
-              ($modalities_subquery==''?'':"$modalities_subquery,") .
-              "s.CenterID as CenterID,
+            ($modalities_subquery==''?'':"$modalities_subquery,") .
+            "s.CenterID as CenterID,
               c.Entity_type as entityType,
               s.ProjectID
-            FROM psc AS p 
-              JOIN session s ON (s.CenterID=p.CenterID) 
-              JOIN candidate c ON (c.CandID=s.CandID) 
+            FROM psc AS p
+              JOIN session s ON (s.CenterID=p.CenterID)
+              JOIN candidate c ON (c.CandID=s.CandID)
               LEFT JOIN Project ON (s.ProjectID=Project.ProjectID)
-              JOIN files f ON (f.SessionID=s.ID) 
-              LEFT JOIN files_qcstatus fqc ON (fqc.FileID=f.FileID) 
+              JOIN files f ON (f.SessionID=s.ID)
+              LEFT JOIN files_qcstatus fqc ON (fqc.FileID=f.FileID)
               JOIN parameter_file pf ON (f.FileID=pf.FileID)
               JOIN parameter_type pt USING (ParameterTypeID)
-              LEFT JOIN mri_scan_type modality ON 
+              LEFT JOIN mri_scan_type modality ON
                 (f.AcquisitionProtocolID=modality.ID)
-              $left_joins 
-            WHERE 
+              $left_joins
+            WHERE
               s.Active = 'Y' AND
               f.FileType IN ('mnc', 'nii')
             GROUP BY s.ID