Removed preprocess function that accidentally got incorporated but was for a custom site. Also removed api function in organism module that didn't fit

tripal_feature/tripal_feature.module

@@ -805,17 +805,15 @@ function chado_feature_form($node, $param) {
    '#options'     => $ftypes,
    '#weight'      => 2
   );
+  
   // get the list of organisms
   $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
   $org_rset = chado_query($sql);
-
-  //
   $organisms = array();
   $organisms[''] = '';
   while ($organism = db_fetch_object($org_rset)) {
     $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
   }
-
   $form['organism_id'] = array(
     '#title'       => t('Organism'),
     '#type'        => t('select'),

tripal_organism/api/tripal_organism.api.inc

@@ -5,30 +5,6 @@
  * Provides an API to tripal organisms
  */
 
-/**
- * Purpose: Create an options array to be used in a form element
- *   which provides a list of all chado organisms
- *
- * @return an array(organism_id => common_name)
- *   for each organism in the chado organism table
- *
- * @ingroup tripal_organism_api
- */
-function tripal_organism_get_organism_options() {
-
-  $result = chado_query(
-    "SELECT organism_id, common_name FROM {organism}"
-  );
-
-  $options = array();
-  while ( $r = db_fetch_object($result) ) {
-    $options[$r->organism_id] = $r->common_name;
-  }
-
-  return $options;
-
-}
-
 /**
  * Purpose: Return a given organism object using the nid
  *

tripal_stock/includes/tripal_stock-administration.inc

@@ -52,9 +52,10 @@ function tripal_stock_admin() {
     );
 
     // get the list of CVs for the next form element
-    $results = tripal_core_chado_select('cv', array('cv_id', 'name'), array());
+    $sql = "SELECT * FROM {cv} ORDER BY name";
+    $results = chado_query($sql);
     $cv_options = array();
-    foreach ($results as $r) {
+    while ($r = db_fetch_object($results)) {
       $cv_options[$r->cv_id] = $r->name;
     }
 
@@ -100,11 +101,19 @@ function tripal_stock_admin() {
          "time to complete. ")
     );
 
+    // get the list of organisms
+    $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
+    $org_rset = chado_query($sql);
+    $organisms = array();
+    $organisms[''] = '';
+    while ($organism = db_fetch_object($org_rset)) {
+      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
+    }
     $form['sync']['organisms'] = array(
       '#type' => 'checkboxes',
       '#title' => t('Organisms for which Stocks should be sync\'d'),
       '#description' => t('Only sync\'d Organisms are listed. Leaving an organism unchecked does not delete already sync\'d Stocks.'),
-      '#options' => tripal_organism_get_organism_options(),
+      '#options' => $organisms,
       '#required'    => FALSE,
       '#prefix'      => '<div id="lib_boxes">',
       '#suffix'      => '</div>'

tripal_stock/tripal_stock.module

@@ -445,16 +445,20 @@ function chado_stock_form($node, $form_state) {
     '#required'    => TRUE,
   );
 
-  $stock_oganism_options = tripal_organism_get_organism_options();
-  $stock_oganism_options[0] = 'Select An Organism';
-  if ($node->nid == '') {
-  $organism_default = 0; }
-  else {  $organism_default = $node->stock->organism_id->organism_id; }
+ 
+  // get the list of organisms
+  $sql = "SELECT * FROM {Organism} ORDER BY genus, species";
+  $org_rset = chado_query($sql);
+  $organisms = array();
+  $organisms[''] = '';
+  while ($organism = db_fetch_object($org_rset)) {
+    $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
+  }
   $form['details']['organism_id'] = array(
     '#type' => 'select',
     '#title' => t('Source Organism for stock'),
     '#default_value' => $organism_default,
-    '#options' => $stock_oganism_options,
+    '#options' => $organisms,
     '#required'    => TRUE
   );
 
@@ -1115,13 +1119,3 @@ function tripal_stock_preprocess_tripal_organism_stocks(&$variables) {
   $organism->stock_browser =  array('stocks' => $stocks, 'pager' => $pager, 'enabled' => TRUE );
 }
 
-/**
- *
- *
- * @ingroup tripal_stock
- */
-function tripal_stock_preprocess_tripal_stock_base(&$variables) {
-	$stock = $variables['node']->stock;
-	$num_seq = db_result(chado_query("SELECT count(*) FROM feature_stock WHERE stock_id = %d", $stock->stock_id));
-	$stock->num_seq = $num_seq;
-}