Tripal 2.0-rc (releae candidate)

tripal_analysis/includes/tripal_analysis.admin.inc

@@ -45,10 +45,6 @@ function tripal_analysis_admin_analysis_view() {
 /**
  * Administration page callbacks for the Tripal Analysis module
  *
- * We have defined a hook_get_settings() function. When a sub-module
- * is enabled, we'll look for this function to provide a form for the
- * administrative setting.
- *
  * @return
  *  A form API array describing an administrative form
  *
@@ -86,7 +82,6 @@ function tripal_analysis_admin() {
     'options' => array(
       '/analysis/[analysis.analysis_id]' => 'Analysis ID',
       '/analysis/[analysis.program]/[analysis.programversion]/[analysis.sourcename]' => 'Unique Contraint: Includes the program name & version as well as the source name'
-
     ),
   );
 
@@ -94,41 +89,6 @@ function tripal_analysis_admin() {
   // This sub-form handles it's own validation & submit
   chado_add_admin_form_set_url($form, $form_state, $details);
 
-  // Add sub-module settings. Pull all sub-module information from
-  // {tripal_analysis} table
-  $sql = "SELECT modulename FROM {tripal_analysis}";
-  $result = db_query($sql);
-  $counter = 0;  //keep track of the number of sub-modules
-  while ($data = $result->fetchObject()) {
-
-    // Check if the hook_get_settings() function is already defined.
-    $func = $data->modulename . "_get_settings";
-    $functions = get_defined_functions();
-    $settings;
-    foreach ($functions['user'] as $function) {
-      if ($function == $func) {
-        $settings = $func();
-      }
-    }
-
-    // Add sub-module's specific settings to the administrative view
-    if ($settings) {
-      // Define a fieldset for the sub-module
-      $form["field$counter"] = array(
-        '#type' => 'fieldset',
-        '#title' => "$settings->title",
-        '#collapsible' => TRUE
-      );
-      $form["field$counter"]["$settings->title"] = $settings->form;
-    }
-    $counter++;
-  }
-
-  if($counter == 0) {
-    $form['nothing'] = array(
-      '#markup' => t('There are currently no settings to configure. However, analysis extension modules may add items here when they are installed.')
-    );
-  }
   return system_settings_form($form);
 }
 

tripal_analysis/includes/tripal_analysis.chado_node.inc

@@ -133,7 +133,7 @@ function chado_analysis_form($node, &$form_state) {
     '#default_value' => $node->title,
   );
   $form['instructions'] = array(
-    '#markup' => t('<b>Note</b>: When adding any type of data it is good to associate it with
+    '#markup' => t('When adding any type of data it is good to associate it with
         an analysis so that site visitors can identify the source of the data including
         necessary materials and methods.  The fields below imply that all analyses
         are derived from some software package. But, data can also be derived via retreival

tripal_core/api/tripal_core.DEPRECATED.inc

@@ -794,7 +794,8 @@ function tripal_job_set_progress($job_id, $percentage) {
 /**
  * @deprecated Restructured API to make naming more readable and consistent.
  * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by tripal_update_mview().
+ * This function has been replaced by tripal_refresh_mview(),  and 
+ * tripal_delete_mview().
  *
  * @see tripal_refresh_mview() or tripal_delete_mview().
  */

tripal_core/api/tripal_core.chado_nodes.title_and_path.inc

@@ -6,7 +6,7 @@
  *
  * TITLES
  * ====================================
- * There are two steps to implement the ability to set custom titles for the node type:
+ * There are three steps to implement the ability to set custom titles for the node type:
  * 1) Add the 'chado_node_api' elements to the hook_node_info function().  These values
  *    define the name of the base table and how to refer to nodes in singular and plural.
  *    There are additional paramaters that can be added to the 'chado_node_api' for
@@ -94,7 +94,7 @@
  *
  * NODE URL/PATHS
  * ====================================
- * There are two steps to implement the ability to set custom URLs for the node type:
+ * There are three steps to implement the ability to set custom URLs for the node type:
  * 1) Add the 'chado_node_api' elements to the hook_node_info function().  These values
  *    define the name of the base table and how to refer to nodes in singular and plural.
  *    There are additional paramaters that can be added to the 'chado_node_api' for

tripal_views/tripal_views.views.inc

@@ -302,7 +302,7 @@ function tripal_views_views_data() {
             functionality for this column. To register handlers, make sure the 'handlers'
             key for this field is set in the integration array (priority = %priority).
             The supported keys include 'field', 'filter', 'sort', 'relationship'. Look
-            at the tripal_views_integration_add_entry() for additional details.",
+            at the tripal_add_views_integration() for additional details.",
           array(
             '%table'=> $base_table,
             '%column' => $column_name,