MRI exclusion scans such as localizers read from the Config module. B…

…asically redoing aces#264. Only took 3 hours of my time today... (aces#319)

uploadNeuroDB/NeuroDB/DBI.pm

@@ -95,7 +95,16 @@ sub getConfigSetting
     $query = $query . $where;
     my $sth = $$dbh->prepare($query);
     $sth->execute($name);
-    if ( $sth->rows > 0 ) {
+
+    if ( $sth->rows > 1 ){
+        # if more than one row returned, push data into an array that will be
+        #  dereferenced into $value
+        my @values;
+        while (my $row = $sth->fetchrow_array()) {
+            push (@values, $row);
+        }
+        $value = \@values;
+    } elsif ( $sth->rows > 0 ) {
         $value = $sth->fetchrow_array();
     }
     return $value;

uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm

@@ -1094,10 +1094,15 @@ sub dicom_to_minc {
 		$exclude,$mail_user, $upload_id) = @_;
     my ($d2m_cmd,$d2m_log,$exit_code);
     my $message = '';
+
+    # create the excluded series description regex necessary to exclude the
+    # series description specified in the Config Setting
+    # excluded_series_description
+    my $excluded_regex = join('|', map { quotemeta($_) } @$exclude);
     $d2m_cmd = "find $study_dir -type f | $get_dicom_info -studyuid -series".
                " -echo -image -file -series_descr -attvalue 0018 0024".
                " -stdin | sort -n -k1 -k2 -k6 -k3 -k7 -k4 | grep -iv".
-               " $exclude | cut -f 5 | ";
+               " -E \"($excluded_regex)\" | cut -f 5 | ";
 
     ############################################################
     #### use some other converter if specified in the config ###

uploadNeuroDB/tarchiveLoader

@@ -273,7 +273,9 @@ my $mail_user = NeuroDB::DBI::getConfigSetting(
 my $get_dicom_info = NeuroDB::DBI::getConfigSetting(
                  \$dbh,'get_dicom_info'
                  );
-my $exclude          = "localizer"; # case insensitive
+my $exclude          = NeuroDB::DBI::getConfigSetting(
+                        \$dbh, 'excluded_series_description'
+                       );
 my $template         = "TarLoad-$hour-$min-XXXXXX"; # for tempdir
 my $User             = `whoami`;