bulk loader no longer counts header line

tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc

@@ -164,10 +164,14 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
     $total_lines++;
   }
   fclose($handle);
+  // do not count header line in the non-blank line count
+  if (($total_lines) and (preg_match('/(t|true|1)/', $node->file_has_header))) {
+    $total_lines--;
+  }
 
   // Correct for files with a single line and no enter character.
   $total_lines = ($total_lines == 0) ? 1 : $total_lines;
-  print "File: " . $node->file . " (" . $total_lines . " lines)\n";
+  print "File: " . $node->file . " (" . $total_lines . " lines with data)\n";
 
   //print "\nClearing all prepared statements from previous runs of this loader...\n";
   //tripal_core_chado_clear_prepared('_'.$node->nid.'_');
@@ -397,7 +401,10 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
 
         // percentage of lines processed for the current group
         $group_progress = round(($num_lines / $total_lines) * 100);
-        tripal_bulk_loader_progress_bar($num_lines, $total_lines);
+        // don't show progress for the last line, that is printed at the end of this function
+        if ($num_lines < $total_lines) {
+          tripal_bulk_loader_progress_bar($num_lines, $total_lines);
+        }
 
         // percentage of lines processed for all groups
         // <previous group index> * 100 + <current group progress>
@@ -476,7 +483,7 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
       $loaded_without_errors = FALSE;
       break;
     }
-    tripal_bulk_loader_progress_bar($total_lines, $total_lines);
+    tripal_bulk_loader_progress_bar($num_lines, $total_lines);
     tripal_bulk_loader_progress_file_track_job($job_id, FALSE, FALSE, TRUE);
   } //end of foreach constant set
 
@@ -528,14 +535,16 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
   }
 
   // Check that template required fields are present. if a required field is
-  // missing and this
-  // is an optional record then just return. otherwise raise an error
+  // missing and this is an optional record then just return. otherwise raise
+  // an error
   $skip_optional = 0;
   foreach ($table_data['required'] as $field => $required) {
+
     if ($required) {
       // check if the field has no value (or array is empty)
       if (!isset($values[$field]) or
         (is_array($values[$field]) and count($values[$field]) == 0)) {
+
         // check if the record is optional.  For backwards compatiblity we need to
         // check if the 'mode' is set to 'optional'
         if ($table_data['optional'] or preg_match('/optional/', $table_data['mode']) or