pkp/pkp-lib#6724 Fix postgres-related issues and missing variable bug

classes/install/Upgrade.inc.php

@@ -121,7 +121,7 @@ public function repairSuppFilesFilestage()
             ->leftJoin('submissions as s', 's.submission_id', '=', 'sf.submission_id')
             ->where('sf.file_stage', '=', SubmissionFile::SUBMISSION_FILE_SUBMISSION)
             ->where('sf.assoc_type', '=', ASSOC_TYPE_REPRESENTATION)
-            ->where('sf.revision', '=', DB::raw('ssf.revision'))
+            ->whereColumn('sf.revision', '=', 'ssf.revision')
             ->get();
 
         foreach ($rows as $row) {
@@ -147,8 +147,8 @@ public function repairSuppFilesFilestage()
                 date('Ymd', strtotime($row->date_uploaded)),
                 strtolower_codesafe($fileManager->parseFileExtension($row->original_file_name))
             );
-            $oldFileName = $submissionDir . '/' . $submissionFileRevision->_fileStageToPath($submissionFileRevision->getFileStage()) . '/' . $generatedOldFilename;
-            $newFileName = $submissionDir . '/' . $submissionFileRevision->_fileStageToPath($submissionFileRevision->getFileStage()) . '/' . $generatedNewFilename;
+            $oldFileName = $submissionDir . '/' . $this->_fileStageToPath($row->file_stage) . '/' . $generatedOldFilename;
+            $newFileName = $submissionDir . '/' . $this->_fileStageToPath($row->file_stage) . '/' . $generatedNewFilename;
             if (!Services::get('file')->fs->rename($oldFileName, $newFileName)) {
                 error_log("Unable to move \"${oldFileName}\" to \"${newFileName}\".");
             }