Changed field names for base fields

tripal_chado/includes/tripal_chado.fields.inc

@@ -98,19 +98,22 @@ function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type,
   // Get the list of columns for this table and create a new field for each one.
   $columns = $schema['fields'];
   foreach ($columns as $column_name => $details) {
-    $field_name = $table_name . '__' . $column_name;
-
-    // Skip fields with a custom field:
-    if ($field_name == 'dbxref_id' or $field_name == 'organism_id') {
-      continue;
-    }
-    if ($table_name == 'feature' and ($field_name == 'md5checksum' or
-        $field_name == 'residues' or $field_name == 'seqlen')) {
-      continue;
-    }
-    if ($table_name == 'organism' and ($field_name == 'type_id')) {
-      continue;
-    }
+    $cvterm = tripal_get_chado_semweb_term($table_name, $column_name, array('return_object' => TRUE));
+    $semweb_term = $cvterm->dbxref_id->db_id->name . ':' . $cvterm->dbxref_id->accession;
+    //$field_name = $table_name . '__' . $column_name;
+    $field_name = strtolower($cvterm->dbxref_id->db_id->name . '__' . preg_replace('/ /', '_', $cvterm->name));
+
+//     // Skip fields with a custom field:
+//     if ($field_name == 'dbxref_id' or $field_name == 'organism_id') {
+//       continue;
+//     }
+//     if ($table_name == 'feature' and ($field_name == 'md5checksum' or
+//         $field_name == 'residues' or $field_name == 'seqlen')) {
+//       continue;
+//     }
+//     if ($table_name == 'organism' and ($field_name == 'type_id')) {
+//       continue;
+//     }
 
     // Skip the primary key field.
     if ($column_name == $schema['primary key'][0]) {
@@ -122,6 +125,7 @@ function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type,
       continue;
     }
 
+
     // Set some defaults for the field.
     $base_info = array(
       'field_name' => $field_name,
@@ -135,7 +139,7 @@ function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type,
         'chado_table' => $table_name,
         'chado_column' => $column_name,
         'base_table' => $table_name,
-        'semantic_web' => tripal_get_chado_semweb_term($table_name, $column_name),
+        'semantic_web' => $semweb_term,
       ),
     );
 
@@ -727,7 +731,10 @@ function tripal_chado_bundle_create_instances_base(&$info, $entity_type, $bundle
 
   $columns = $schema['fields'];
   foreach ($columns as $column_name => $details) {
-    $field_name = $table_name . '__' . $column_name;
+    $cvterm = tripal_get_chado_semweb_term($table_name, $column_name, array('return_object' => TRUE));
+    $semweb_term = $cvterm->dbxref_id->db_id->name . ':' . $cvterm->dbxref_id->accession;
+    //$field_name = $table_name . '__' . $column_name;
+    $field_name = strtolower($cvterm->dbxref_id->db_id->name . '__' . preg_replace('/ /', '_', $cvterm->name));
 
     // Skip the primary key field.
     if ($column_name == $schema['primary key'][0]) {