Bulk Loader: Updated loader to use new tripal_core_report_error function and print errors to the screen in addition to adding them to watchdog. Hopefully this makes errors easier to read when transactions fail, etc.

tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc

@@ -280,13 +280,13 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
             }
             else {
               print "ERROR: Template has changed after constants were assigned!\n";
-              watchdog('T_bulk_loader', 'Template has changed after constants were assigned', array(), WATCHDOG_NOTICE);
+              tripal_bulk_loader_throw_error('Template has changed after constants were assigned', array(), WATCHDOG_NOTICE);
               exit(1);
             }
           }
           else {
             print "ERROR: Template has changed after constants were assigned!\n";
-            watchdog('T_bulk_loader', 'Template has changed after constants were assigned', array(), WATCHDOG_NOTICE);
+            tripal_bulk_loader_throw_error('Template has changed after constants were assigned', array(), WATCHDOG_NOTICE);
             exit(1);
           }
         }
@@ -300,8 +300,8 @@ function tripal_bulk_loader_load_data($nid, $job_id) {
       $file = new SplFileObject($node->file, 'r');
     }
     catch (Exception $e) {
-      watchdog('T_bulk_loader', 'Could not open file %file',
-        array($node->file), WATCHDOG_ERROR);
+      tripal_bulk_loader_throw_error('Could not open file %file',
+        array('%file' => $node->file), WATCHDOG_ERROR);
       return;
     }
 
@@ -512,14 +512,15 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
 
   $values = tripal_bulk_loader_regex_tranform_values($values, $table_data, $addt->line);
   if (!$values) {
-    //watchdog('T_bulk_loader', 'Line ' . $addt->line_num . ' Regex:<pre>' . print_r($values, TRUE) . print_r($table_data, TRUE) . '</pre>' . '</pre>', array(), WATCHDOG_NOTICE);
+    //tripal_bulk_loader_throw_error('Line ' . $addt->line_num . ' Regex:<pre>' . print_r($values, TRUE) . print_r($table_data, TRUE) . '</pre>' . '</pre>', array(), WATCHDOG_NOTICE);
   }
 
   // get the table description
   $table_desc = tripal_core_get_chado_table_schema($table);
   if (!$table_desc) {
-    watchdog('T_bulk_loader', "Failure: Tripal does not know about the table named '%table'. If this is a custom table,
-      please define it first", array('%table' => $table), WATCHDOG_ERROR);
+    $msg = "Tripal does not know about the table named '%table'. If this is a custom table,
+      please define it first";
+    tripal_bulk_loader_throw_error($msg,  array('%table' => $table), WATCHDOG_ERROR);
     $data[$priority]['error'] = TRUE;
     return;
   }
@@ -546,7 +547,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
         else {
           $msg = "\nLine " . $addt->line_num . ' "' . $table_data['record_id'] .
             '" (' . $table_data['mode'] . ') Missing template required value: ' . $table . '.' . $field;
-          watchdog('T_bulk_loader', $msg, array(), WATCHDOG_WARNING);
+          tripal_bulk_loader_throw_error($msg, array(), WATCHDOG_WARNING);
           $data[$priority]['error'] = TRUE;
           $no_errors = FALSE;
         }
@@ -570,7 +571,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
           strcmp($def['type'], 'serial') != 0) {                             // it is not a 'serial' type column
         $msg = "\nLine " . $addt->line_num . ' ' . $table_data['record_id'] .
                ' (' . $table_data['mode'] . ') Missing Database Required Value: ' . $table . '.' . $field;
-        watchdog('T_bulk_loader', $msg, array(), WATCHDOG_ERROR);
+        tripal_bulk_loader_throw_error($msg, array(), WATCHDOG_ERROR);
         $data[$priority]['error'] = TRUE;
       }
     }
@@ -581,19 +582,19 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
 
   // if there was an error already -> don't insert
   if (array_key_exists('error', $data[$priority]) and $data[$priority]['error']) {
-    watchdog('T_bulk_loader','Skipping processing of %table due to previous errors',array('%table'=>$table),WATCHDOG_NOTICE);
+    tripal_bulk_loader_throw_error('Skipping processing of %table due to previous errors',array('%table'=>$table),WATCHDOG_NOTICE);
     return $no_errors;
   }
 
   // skip optional fields
   if ($skip_optional) {
-    watchdog('T_bulk_loader','Skipping an optional record (%record)',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
+    tripal_bulk_loader_throw_error('Skipping an optional record (%record)',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
     return $no_errors;
   }
 
   // check if it is already inserted
   if (array_key_exists('inserted', $table_data) and $table_data['inserted']) {
-    watchdog('T_bulk_loader','Skipping %record since it is already inserted',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
+    tripal_bulk_loader_throw_error('Skipping %record since it is already inserted',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
     return $no_errors;
   }
 
@@ -601,7 +602,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
   // the default_data array
   if (array_key_exists('selected', $table_data) and $table_data['selected']) {
     $data[$priority]['values_array'] = $default_data[$priority]['values_array'];
-    watchdog('T_bulk_loader','%record was already selected thus we are just returning the values previously selected.',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
+    tripal_bulk_loader_throw_error('%record was already selected thus we are just returning the values previously selected.',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
     return $no_errors;
   }
 
@@ -620,7 +621,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
   if (preg_match('/insert_unique/', $table_data['mode']) or
      $table_data['select_if_duplicate'] == 1 or
      $table_data['update_if_duplicate'] == 1) {
-    $options = array('is_duplicate' => TRUE);
+    $options = array('is_duplicate' => TRUE, 'print_errors' => TRUE);
     $duplicate = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values, $options);
 
     // if this is a duplicate then substitute the values in the table_data array so
@@ -652,7 +653,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
       }
       // return if this is a select_if_duplicate
       if ($table_data['select_if_duplicate'] == 1) {
-        watchdog('T_bulk_loader','Simply returning values for %record since it was already inserted',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
+        tripal_bulk_loader_throw_error('Simply returning values for %record since it was already inserted',array('%record'=>$table_data['record_id']),WATCHDOG_NOTICE);
         return $no_errors;
       }
     }
@@ -708,14 +709,16 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
 			}
 			if (!empty($match)) {
 				// Now we need to check if it already exists via a select
-				$results = tripal_core_chado_select($table, array_keys($table_desc['fields']), $match);
+				$results = tripal_core_chado_select($table, array_keys($table_desc['fields']), $match, array('print_errors' => TRUE));
 				// If not then insert
 				if (empty($results)) {
 					$options['statement_name'] = 'ins_'.$options['statement_name'];
+					$options['print_errors'] = TRUE;
 					$record = tripal_core_chado_insert($table, $values, $options);
 				}
 				else {
 				  $options['return_record'] = TRUE;
+				  $options['print_errors'] = TRUE;
   		    $record = tripal_core_chado_update($table, $match, $values, $options);
   		  }
   	  }
@@ -724,12 +727,13 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
         $table_data['mode'] . ') Unable to update record since none of the unique key or primary key fields were available ' .
         ' where values:' . print_r($values, TRUE);
 
-      	watchdog('T_bulk_loader', $msg, array(), WATCHDOG_ERROR);
+      	tripal_bulk_loader_throw_error($msg, array(), WATCHDOG_ERROR);
       	$data[$priority]['error'] = TRUE;
       	$no_errors = FALSE;
   	  }
     }
     else {
+      $options['print_errors'] = TRUE;
       $record = tripal_core_chado_insert($table, $values, $options);
     }
 
@@ -739,7 +743,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
         $table_data['mode'] . ') Unable to insert record into ' . $table .
         ' where values:' . print_r($values, TRUE);
 
-      watchdog('T_bulk_loader', $msg, array(), WATCHDOG_ERROR);
+      tripal_bulk_loader_throw_error($msg, array(), WATCHDOG_ERROR);
       $data[$priority]['error'] = TRUE;
       $no_errors = FALSE;
     }
@@ -798,14 +802,14 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
     // get the matches for this select
     $matches = array();
     if (is_array($values) and count($values) > 0) {
-      $matches = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values);
+      $matches = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values, array('print_errors' => TRUE));
     }
     // if the record doesn't exist and it's not optional then generate an error
     if (count($matches) == 0) {
       // No record on select
       if ($table_data['select_optional'] != 1) {
         $msg = "\nLine " . $addt->line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') No Matching record in ' . $table . ' where values:' . print_r($values, TRUE);
-        watchdog('T_bulk_loader', $msg, array(), WATCHDOG_ERROR);
+        tripal_bulk_loader_throw_error($msg, array(), WATCHDOG_ERROR);
         $data[$priority]['error'] = TRUE;
         $no_errors = FALSE;
       }
@@ -819,7 +823,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
     if (count($matches) > 1) {
       if ($table_data['select_optional'] != 1) {
         $msg = "\nLine " . $addt->line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') Too many matching records in ' . $table . ' where values:' . print_r($values, TRUE);
-        watchdog('T_bulk_loader', $msg, array(), WATCHDOG_WARNING);
+        tripal_bulk_loader_throw_error($msg, array(), WATCHDOG_WARNING);
         $data[$priority]['error'] = TRUE;
         $no_errors = FALSE;
       }
@@ -927,6 +931,7 @@ function tripal_bulk_loader_add_foreignkey_to_values($table_array, $values, $dat
           array_key_exists($foreign_table, $tbl_description['foreign keys']) and
           array_key_exists($field, $tbl_description['foreign keys'][$foreign_table]['columns']) and
           $foreign_field == $tbl_description['foreign keys'][$foreign_table]['columns'][$field]) {
+          //check here for fk bug
          $values[$field] = $foreign_values;
       }
       // if the field in the Referral records is not in an FK relationship
@@ -942,6 +947,7 @@ function tripal_bulk_loader_add_foreignkey_to_values($table_array, $values, $dat
             $fvalues = array($fk_description['primary key'][0] => $foreign_values);
             $columns = array($foreign_field);
             $options = array('statement_name' => 'pk_' . $foreign_table);
+            $options['print_errors'] = TRUE;
             $record  = tripal_core_chado_select($foreign_table, $columns, $fvalues, $options);
             if ($record) {
               $values[$field] = $record[0]->$foreign_field;
@@ -962,6 +968,7 @@ function tripal_bulk_loader_add_foreignkey_to_values($table_array, $values, $dat
           $fvalues  = $foreign_values;
           $columns = array($foreign_field);
           $options = array('statement_name' => 'blk_' . $nid . $priority . $foreign_table);
+          $options['print_errors'] = TRUE;
           $record  = tripal_core_chado_select($foreign_table, $columns, $fvalues, $options);
           if ($record) {
             $values[$field] = $record[0]->$foreign_field;
@@ -1167,3 +1174,13 @@ function tripal_bulk_loader_progress_file_track_job($job_id, $record_added, $lin
     variable_set('tripal_bulk_loader_progress_file_handle', NULL);
   }
 }
+
+function tripal_bulk_loader_throw_error($msg, $args, $severity) {
+  tripal_core_report_error(
+    'tripal_bulk',
+    $severity,
+    $msg,
+    $args,
+    array('print' => TRUE)
+  );
+}