From eb0910ec614927c291534c14edd11daccfd7a32d Mon Sep 17 00:00:00 2001
From: MounaSafiHarab <mouna.safiharab@gmail.com>
Date: Wed, 28 Sep 2016 09:14:09 -0400
Subject: [PATCH] Added a ScannerID column to files table: Redmine 10939 (#156)

* Added a ScannerCandID column to files table: Redmine 10939

* Populate ScannerID not ScannerCandID

* better way to populate the scannerID in files table

* updated DTIPrep files
---
 uploadNeuroDB/NeuroDB/MRI.pm             |  2 +-
 uploadNeuroDB/minc_insertion.pl          |  2 +-
 uploadNeuroDB/registerFile.pl            |  2 +-
 uploadNeuroDB/register_processed_data.pl | 11 +++++------
 4 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/uploadNeuroDB/NeuroDB/MRI.pm b/uploadNeuroDB/NeuroDB/MRI.pm
index 5fcc19b4e..362f11c48 100755
--- a/uploadNeuroDB/NeuroDB/MRI.pm
+++ b/uploadNeuroDB/NeuroDB/MRI.pm
@@ -718,7 +718,7 @@ sub register_db {
     # build the insert query
     my $query = "INSERT INTO files SET ";
 
-    foreach my $key ('File', 'SessionID','EchoTime', 'CoordinateSpace', 'OutputType', 'AcquisitionProtocolID', 'FileType', 'InsertedByUserID', 'Caveat', 'SeriesUID', 'TarchiveSource','SourcePipeline','PipelineDate','SourceFileID') {
+    foreach my $key ('File', 'SessionID','EchoTime', 'CoordinateSpace', 'OutputType', 'AcquisitionProtocolID', 'FileType', 'InsertedByUserID', 'Caveat', 'SeriesUID', 'TarchiveSource','SourcePipeline','PipelineDate','SourceFileID', 'ScannerID') {
         # add the key=value pair to the query
         $query .= "$key=".$dbh->quote($${fileData{$key}}).", ";
     }
diff --git a/uploadNeuroDB/minc_insertion.pl b/uploadNeuroDB/minc_insertion.pl
index e0d018814..57ee4b923 100755
--- a/uploadNeuroDB/minc_insertion.pl
+++ b/uploadNeuroDB/minc_insertion.pl
@@ -378,7 +378,7 @@
 ## at this point things will appear in the database ############
 ## Set some file information ###################################
 ################################################################
-$file->setParameter('ScannerID', $scannerID);
+$file->setFileData('ScannerID', $scannerID);
 $file->setFileData('SessionID', $sessionID);
 $file->setFileData('SeriesUID', $file->getParameter('series_instance_uid'));
 $file->setFileData('EchoTime', $file->getParameter('echo_time'));
diff --git a/uploadNeuroDB/registerFile.pl b/uploadNeuroDB/registerFile.pl
index 08e1d0279..d447afa03 100755
--- a/uploadNeuroDB/registerFile.pl
+++ b/uploadNeuroDB/registerFile.pl
@@ -176,7 +176,7 @@
 												$file->getParameter('software_versions'),
 												$centerID,
 												\$dbh, 0);
-	$file->setParameter('ScannerID', $scannerID);
+	$file->setFileData('ScannerID', $scannerID);
     print "Set scannerid = $scannerID\n" if $verbose;
 	
 	# get ids from the headers
diff --git a/uploadNeuroDB/register_processed_data.pl b/uploadNeuroDB/register_processed_data.pl
index bd69f8192..bbb9a4376 100755
--- a/uploadNeuroDB/register_processed_data.pl
+++ b/uploadNeuroDB/register_processed_data.pl
@@ -168,7 +168,7 @@
     print LOG "\nERROR: could not determine scannerID based on sourceFileID $sourceFileID.\n\n";
     exit 2;
 }
-$file->setParameter('ScannerID',$scannerID);
+$file->setFileData('ScannerID',$scannerID);
 print LOG "\t -> Set ScannerID to $scannerID.\n";
 
 
@@ -302,16 +302,15 @@ sub getSessionID    {
 
 
 =pod
-This function gets ScannerID from parameter_file using sourceFileID
+This function gets ScannerID from files using sourceFileID
 =cut
 sub getScannerID    {
     my  ($sourceFileID,$dbh)    =   @_;    
 
     my $scannerID;
-    my $query   =   "SELECT pf.Value AS ScannerID " .
-                    "FROM parameter_file AS pf " .
-                    "JOIN parameter_type AS pt ON (pt.ParameterTypeID=pf.ParameterTypeID) " .
-                    "WHERE pt.Name='ScannerID' AND pf.FileID=?";
+    my $query   =   "SELECT f.ScannerID AS ScannerID " .
+                    "FROM files AS f " .
+                    "WHERE f.FileID=?";
     my $sth     =   $dbh->prepare($query);
     $sth->execute($sourceFileID);
     if($sth->rows > 0) {