Merge branch '7.x-3.x' of github.com:tripal/tripal into 7.x-3.x

README.md

@@ -54,7 +54,8 @@ are available in Tripal v3.
     * [Views](http://drupal.org/project/views)
     * [Entity API](http://drupal.org/project/entity)
 * PostgreSQL
-* UNIX/Linux  
+* PHP 5.5+
+* UNIX/Linux
 
 
 # Installation

tripal/includes/TripalEntityUIController.inc

@@ -751,6 +751,7 @@ function tripal_entity_form_ajax_callback($form, $form_state) {
   * Submit callback for tripal_entity_delete_form
   */
  function tripal_entity_delete_form_submit($form, &$form_state) {
+   global $user;
    $entity = $form_state['entity'];
 
    if (!entity_access('delete', 'TripalEntity', $entity, $user)) {

tripal_chado/api/tripal_chado.api.inc

@@ -386,7 +386,7 @@ function tripal_get_chado_entity_id ($chado_table, $record_id) {
     $type_id = NULL;
     if (key_exists($type_column, $schema['fields'])) {
       $type_id =
-        chado_db_select($chado_table, 'C')
+        db_select("chado.$chado_table", 'C')
           ->fields('C', array($type_column))
           ->condition($pkey, $record_id)
           ->execute()

tripal_chado/includes/TripalFields/sbo__phenotype/sbo__phenotype_formatter.inc

@@ -42,6 +42,7 @@ class sbo__phenotype_formatter extends ChadoFieldFormatter {
     }
     foreach ($items as $delta => $item) {
       $row = array();
+      $phenotype = $item['value'];
       if ($has_type) {
         $row[] = $phenotype['type'];
       }

tripal_chado/includes/TripalFields/so__genotype/so__genotype_formatter.inc

@@ -25,9 +25,9 @@ class so__genotype_formatter extends ChadoFieldFormatter {
       }
 
       // Get the field values
-      $genotype_name = $genotype['name'];
-      $description = $genotype['description'];
-      $type = $genotype['type'];
+      $genotype_name = $genotype['schema:name'];
+      $description = $genotype['schema:description'];
+      $type = $genotype['rdfs:type'];
 
       // Add a link i there is an entity.
       if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {

tripal_chado/includes/TripalImporter/GFF3Importer.inc

@@ -1231,7 +1231,7 @@ class GFF3Importer extends TripalImporter {
             'fmax' => $fmax,
             'strand' => $strand,
           );
-          if ($phase) {
+          if (isset($phase)) {
             $values['phase'] = $phase;
           }
           $result = chado_insert_record('tripal_gffcds_temp', $values);