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

tripal_chado/api/modules/tripal_chado.db.api.inc

@@ -331,7 +331,7 @@ function tripal_insert_db($values, $options = array()) {
       tripal_report_error('tripal_chado', TRIPAL_WARNING, "Cannot create db '$dbname'.", NULL);
       return 0;
     }
-    $result = chado_select_record('db', array('*'), $sel_values, $sel_options);
+    $result = chado_select_record('db', array('*'), $sel_values);
   }
   // if it exists and update is enabled the do the update
   elseif ($update) {
@@ -341,7 +341,7 @@ function tripal_insert_db($values, $options = array()) {
       tripal_report_error('tripal_chado', TRIPAL_WARNING, "Cannot update db '$dbname'.", NULL);
       return 0;
     }
-    $result = chado_select_record('db', array('*'), $sel_values, $sel_options);
+    $result = chado_select_record('db', array('*'), $sel_values);
   }
 
   // return the database object

tripal_chado/includes/loaders/tripal_chado.obo_loader.inc

@@ -1424,7 +1424,7 @@ function tripal_cv_obo_add_dbxref($db_id, $accession, $version='', $description=
       tripal_cv_obo_quiterror("Failed to insert the dbxref record $accession");
       return FALSE;
     }
-    $result = chado_select_record('dbxref', array('dbxref_id'), $values, $options);
+    $result = chado_select_record('dbxref', array('dbxref_id'), $values);
   }
   return $result[0];
 }

tripal_chado/includes/tripal_chado.setup.inc

@@ -725,40 +725,40 @@ function tripal_chado_install_sql($sql_file) {
     if (strcmp($stack[sizeof($stack)-1], 'table') == 0 and preg_match('/\);\s*$/', $line)) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'alter table') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'alter table') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'set') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'set') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'schema') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'schema') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'sequence') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'sequence') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'view') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'view') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'comment') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'comment') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'function') == 0 and preg_match("/LANGUAGE.*?;\s+$/i", $line)) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'function') == 0 and preg_match("/LANGUAGE.*?;\s+$/i", $line)) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'index') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'index') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'insert') == 0 and preg_match('/\);\s*$/', $line)) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'insert') == 0 and preg_match('/\);\s*$/', $line)) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'type') == 0 and preg_match('/\);\s*$/', $line)) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'type') == 0 and preg_match('/\);\s*$/', $line)) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'grant') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'grant') == 0 and preg_match('/;\s*$/', $line) and !$in_string) {
       $type = array_pop($stack);
     }
-    if (strcmp($stack[sizeof($stack)-1], 'aggregate') == 0 and preg_match('/\);\s*$/', $line)) {
+    elseif (strcmp($stack[sizeof($stack)-1], 'aggregate') == 0 and preg_match('/\);\s*$/', $line)) {
       $type = array_pop($stack);
     }
     // if we're in a recognized SQL statement then let's keep track of lines