Fixed parsing bug in GFF loader. Moved all include files into an include directory

tripal_feature/gff_loader.php → tripal_feature/includes/gff_loader.inc

@@ -361,13 +361,13 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id, $add_on
       if (strcmp($attr, '')==0) {
         continue;
       }
-      if (!preg_match('/^[^\=]+\=[^\=]+$/', $attr)) {
+      if (!preg_match('/^[^\=]+\=.+$/', $attr)) {
         print "ERROR: attribute is not correctly formatted on line $line_num: $attr\n";
         return '';
       }
 
       // break apart each tag
-      $tag = explode("=", $attr);  // split by equals sign
+      $tag = preg_split("/=/", $attr,2);  // split by equals sign
       // multiple instances of an attribute are separated by commas
       $tags[$tag[0]] = explode(",", $tag[1]);  // split by comma
       if (strcmp($tag[0], 'ID')==0) {

tripal_feature/tripal_feature.module

@@ -13,19 +13,19 @@
  * @ingroup tripal_modules
  */
 
-require_once "tripal_feature.admin.inc";
-require_once "syncFeatures.php";
-require_once "indexFeatures.php";
-require_once "fasta_loader.php";
-require_once "gff_loader.php";
-
-require_once "tripal_feature.api.inc";
-
-require_once "tripal_feature-delete.inc";
-require_once "tripal_feature-secondary_tables.inc";
-require_once "tripal_feature-properties.inc";
-require_once "tripal_feature-relationships.inc";
-require_once "tripal_feature-db_references.inc";
+require_once "includes/tripal_feature.admin.inc";
+require_once "includes/syncFeatures.inc";
+require_once "includes/indexFeatures.inc";
+require_once "includes/fasta_loader.inc";
+require_once "includes/gff_loader.inc";
+
+require_once "includes/tripal_feature.api.inc";
+
+require_once "includes/tripal_feature-delete.inc";
+require_once "includes/tripal_feature-secondary_tables.inc";
+require_once "includes/tripal_feature-properties.inc";
+require_once "includes/tripal_feature-relationships.inc";
+require_once "includes/tripal_feature-db_references.inc";
 
 
 /**