Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x

tripal_analysis/includes/tripal_analysis.chado_node.inc

@@ -613,17 +613,36 @@ function tripal_analysis_node_view($node, $view_mode, $langcode) {
  * @param $node
  */
 function tripal_analysis_node_presave($node) {
-  // If this is an analysis of some type it will should have thre three required
+  // If this is an analysis of some type it will should have three required
   // fields for the Chado analysis table: program, programversion and sourcename.
-  // So we will set the title for any node that has these three fields
+  // So we will set the title for any node that has these three fields. Some extension
+  // modules will use this module as a type of "inherited" class, so we don't know
+  // for sure when type of analysis we have.
   if (property_exists($node, 'program') and
-  property_exists($node, 'programversion') and
-  property_exists($node, 'sourcename')) {
-    if ($node->analysisname) {
-      $node->title = $node->analysisname;
+      property_exists($node, 'programversion') and
+      property_exists($node, 'sourcename')) {
+    $name = '';
+    $program = '';
+    $programversion = '';
+    $sourcename = '';
+    if (property_exists($node, 'analysis')) {
+      $name           = $node->analysis->name;
+      $program        = $node->analysis->program;
+      $programversion = $node->analysis->programversion;
+      $sourcename     = $node->analysis->sourcename;
     }
     else {
-      $node->title = "$node->program ($node->programversion) $node->sourcename";
+      $name           = $node->analysisname;
+      $program        = $node->program;
+      $programversion = $node->programversion;
+      $sourcename     = $node->sourcename;
+    }
+    // now construct the title
+    if ($name) {
+      $node->title = $name;
+    }
+    else {
+      $node->title = "$program ($programversion) $sourcename";
     }
   }
 }

tripal_analysis/tripal_analysis.module

@@ -39,7 +39,7 @@ function tripal_analysis_menu() {
     'title' => 'Analyses',
     'description' => 'A bioinformatics analysis producing features.',
     'page callback' => 'tripal_analysis_admin_analysis_view',
-    'access arguments' => array('administer tripal analyses'),
+    'access arguments' => array('administer tripal analysis'),
     'type' => MENU_NORMAL_ITEM,
   );
 
@@ -48,7 +48,7 @@ function tripal_analysis_menu() {
     'description' => "A description of the Tripal Analysis module including a short description of it's usage.",
     'page callback' => 'theme',
     'page arguments' => array('tripal_analysis_help'),
-    'access arguments' => array('administer tripal analyses'),
+    'access arguments' => array('administer tripal analysis'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10,
   );
@@ -58,7 +58,7 @@ function tripal_analysis_menu() {
     'description' => 'Settings for the displays of analysis results.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_analysis_admin'),
-    'access arguments' => array('administer tripal analyses'),
+    'access arguments' => array('administer tripal analysis'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );

tripal_bulk_loader/api/tripal_bulk_loader.api.templates.inc

@@ -44,9 +44,9 @@ function tripal_bulk_loader_is_record_name_unique($new_record_name, $template_id
   // Check the new record name is unique
   foreach ($template_array as $priority => $t) {
     if (strcmp($t['record_id'], $new_record_name) == 0) {
-    	if (($priority != $current_priority) AND ($current_priority !== NULL)) {
-	      return FALSE;
-	    }
+      if (($priority != $current_priority) AND ($current_priority !== NULL)) {
+        return FALSE;
+      }
     }
   }
   return TRUE;
@@ -67,21 +67,21 @@ function tripal_bulk_loader_is_record_name_unique($new_record_name, $template_id
  */
 function tripal_bulk_loader_delete_record($delete_priority, $template_array) {
 
-	if (empty($template_array)) {
-		drupal_set_message("Unable to delete record with a priority of $priority since the template was not supplied",'error');
-		return FALSE;
-	}
+  if (empty($template_array)) {
+    drupal_set_message("Unable to delete record with a priority of $priority since the template was not supplied",'error');
+    return FALSE;
+  }
 
-	$new_template_array = array();
-	$i=0;
-	foreach ($template_array as $priority => $record) {
-		if ($priority != $delete_priority) {
-			$new_template_array[$i] = $record;
-			$i++;
-		}
-	}
+  $new_template_array = array();
+  $i=0;
+  foreach ($template_array as $priority => $record) {
+    if ($priority != $delete_priority) {
+      $new_template_array[$i] = $record;
+      $i++;
+    }
+  }
 
-	return $new_template_array;
+  return $new_template_array;
 }
 
 /**
@@ -101,27 +101,27 @@ function tripal_bulk_loader_delete_record($delete_priority, $template_array) {
  */
 function tripal_bulk_loader_delete_field($priority, $delete_field_index, $template_array) {
 
-	if (empty($template_array)) {
-		drupal_set_message("Unable to delete record with a priority of $priority since the template was not supplied",'error');
-		return FALSE;
-	}
+  if (empty($template_array)) {
+    drupal_set_message("Unable to delete record with a priority of $priority since the template was not supplied",'error');
+    return FALSE;
+  }
 
-	// Re-order the remaining fields of the same record to ensure that the indicies are
-	// 0 to size and. If this is not done, weird behaviour may result
-	$new_template_array = $template_array;
-	$new_template_array[$priority]['fields'] = array();
-	$i=0;
-	foreach ($template_array[$priority]['fields'] as $field_index => $field_details) {
-		if ($field_index != $delete_field_index) {
-			$new_template_array[$priority]['fields'][$i] = $field_details;
-			$i++;
-		}
-	}
+  // Re-order the remaining fields of the same record to ensure that the indicies are
+  // 0 to size and. If this is not done, weird behaviour may result
+  $new_template_array = $template_array;
+  $new_template_array[$priority]['fields'] = array();
+  $i=0;
+  foreach ($template_array[$priority]['fields'] as $field_index => $field_details) {
+    if ($field_index != $delete_field_index) {
+      $new_template_array[$priority]['fields'][$i] = $field_details;
+      $i++;
+    }
+  }
 
-	// If this field was the only one in the current record, also delete the record
-	if (empty($new_template_array[$priority]['fields'])) {
-		$new_template_array = tripal_bulk_loader_delete_record($priority, $new_template_array);
-	}
+  // If this field was the only one in the current record, also delete the record
+  if (empty($new_template_array[$priority]['fields'])) {
+    $new_template_array = tripal_bulk_loader_delete_record($priority, $new_template_array);
+  }
 
-	return $new_template_array;
+  return $new_template_array;
 }

tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc

@@ -2368,9 +2368,9 @@ function tripal_bulk_loader_delete_template_field_form_submit($form, &$form_stat
     $form_state['storage']['field_id'],
     $form_state['storage']['template']
   );
-	if (!empty($new_template)) {
-		$form_state['storage']['template'] = $new_template;
-	}
+  if (!empty($new_template)) {
+    $form_state['storage']['template'] = $new_template;
+  }
   drupal_set_message(t('Deleted Field from Template.'));
 
   $record = array(

tripal_bulk_loader/includes/tripal_bulk_loader.loader.inc

@@ -672,51 +672,51 @@ function process_data_array_for_line($priority, &$data, &$default_data, $addt) {
       // This should have been set on the first round of inserts for this record
       $match = $data[$priority]['is_duplicate'];
       // However, sometimes there is a pre-existing record before the loader starts
-			// Thus check that this value is set and if not, then generate a match array
-			// based on the unique keys for this record.
-			if (empty($match)) {
-				$match = array();
-				// First check to see if we have fields for the primary key
-				foreach ($table_desc['primary key'] as $k_field) {
-					if (!empty($values[$k_field])) {
-						$match[$k_field] = $values[$k_field];
-					}
-				}
-				// Otherwise check the fields that are part of the unique key
-				if (empty($match)) {
-					foreach ($table_desc['unique keys'] as $u_keys) {
-						foreach ($u_keys as $u_field) {
-							if (!empty($values[$u_field])) {
-								$match[$u_field] = $values[$u_field];
-							}
-						}
-					}
-				}
-			}
-			if (!empty($match)) {
-				// Now we need to check if it already exists via a select
-				$results = tripal_core_chado_select($table, array_keys($table_desc['fields']), $match, array('print_errors' => TRUE));
-				// If not then insert
-				if (empty($results)) {
-					$options['statement_name'] = 'ins_'.$options['statement_name'];
-					$options['print_errors'] = TRUE;
-					$record = tripal_core_chado_insert($table, $values, $options);
-				}
-				else {
-				  $options['return_record'] = TRUE;
-				  $options['print_errors'] = TRUE;
-  		    $record = tripal_core_chado_update($table, $match, $values, $options);
-  		  }
-  	  }
-  	  else {
-  	  	$msg = "\nLine " . $addt->line_num . ' ' . $table_data['record_id'] . ' (' .
+      // Thus check that this value is set and if not, then generate a match array
+      // based on the unique keys for this record.
+      if (empty($match)) {
+        $match = array();
+        // First check to see if we have fields for the primary key
+        foreach ($table_desc['primary key'] as $k_field) {
+          if (!empty($values[$k_field])) {
+            $match[$k_field] = $values[$k_field];
+          }
+        }
+        // Otherwise check the fields that are part of the unique key
+        if (empty($match)) {
+          foreach ($table_desc['unique keys'] as $u_keys) {
+            foreach ($u_keys as $u_field) {
+              if (!empty($values[$u_field])) {
+                $match[$u_field] = $values[$u_field];
+              }
+            }
+          }
+        }
+      }
+      if (!empty($match)) {
+        // Now we need to check if it already exists via a select
+        $results = tripal_core_chado_select($table, array_keys($table_desc['fields']), $match, array('print_errors' => TRUE));
+        // If not then insert
+        if (empty($results)) {
+          $options['statement_name'] = 'ins_'.$options['statement_name'];
+          $options['print_errors'] = TRUE;
+          $record = tripal_core_chado_insert($table, $values, $options);
+        }
+        else {
+          $options['return_record'] = TRUE;
+          $options['print_errors'] = TRUE;
+          $record = tripal_core_chado_update($table, $match, $values, $options);
+        }
+      }
+      else {
+        $msg = "\nLine " . $addt->line_num . ' ' . $table_data['record_id'] . ' (' .
         $table_data['mode'] . ') Unable to update record since none of the unique key or primary key fields were available ' .
         ' where values:' . print_r($values, TRUE);
 
-      	tripal_bulk_loader_throw_error($msg, array(), TRIPAL_ERROR);
-      	$data[$priority]['error'] = TRUE;
-      	$no_errors = FALSE;
-  	  }
+        tripal_bulk_loader_throw_error($msg, array(), TRIPAL_ERROR);
+        $data[$priority]['error'] = TRUE;
+        $no_errors = FALSE;
+      }
     }
     else {
       $options['print_errors'] = TRUE;

tripal_bulk_loader/theme/node--tripal-bulk-loader.tpl.php

@@ -1,45 +1,45 @@
 <div id="tripal_bulk_loader-base-box" class="tripal_bulk_loader-info-box tripal-info-box">
   <div class="tripal_bulk_loader-info-box-title tripal-info-box-title">
-  	<?php if ($teaser) { print l($node->title, 'node/'.$node->nid); } ?>
+    <?php if ($teaser) { print l($node->title, 'node/'.$node->nid); } ?>
   </div>
   <div class="tripal_bulk_loader-info-box-desc tripal-info-box-desc"></div>
 
-	<table id="tripal_bulk_loader-base-table" class="tripal_bulk_loader-table tripal-table tripal-table-vert">
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Job Name</th>
-			<td><?php print $node->loader_name;?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
-			<th>Submitted By</th>
-			<td><span class="author"><?php //print theme('username', $node); ?></span></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Job Creation Date</th>
-			<td><?php print format_date($node->created, 'custom', "F j, Y, g:i a"); ?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
-			<th>Last Updated</th>
-			<td><?php print format_date($node->changed, 'custom', "F j, Y, g:i a"); ?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Template Name</th>
-			<td><?php print $node->template->name; ?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
-			<th>Data File</th>
-			<td><?php print $node->file;?></td>
-		</tr>
-		<tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
-			<th>Job Status</th>
-			<td><?php print $node->job_status;?></td>
-		</tr>
-		<?php if (isset($node->job)) { if (isset($node->job->progress)) { ?>
-		<tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
-			<th>Job Progress</th>
-			<td><?php print $node->job->progress . '% (' . l('view job', 'admin/tripal/tripal_jobs/view/' . $node->job_id) . ')';?></td>
-		</tr>
-		<?php }} ?>
-	</table>
+  <table id="tripal_bulk_loader-base-table" class="tripal_bulk_loader-table tripal-table tripal-table-vert">
+    <tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
+      <th>Job Name</th>
+      <td><?php print $node->loader_name;?></td>
+    </tr>
+    <tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
+      <th>Submitted By</th>
+      <td><span class="author"><?php //print theme('username', $node); ?></span></td>
+    </tr>
+    <tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
+      <th>Job Creation Date</th>
+      <td><?php print format_date($node->created, 'custom', "F j, Y, g:i a"); ?></td>
+    </tr>
+    <tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
+      <th>Last Updated</th>
+      <td><?php print format_date($node->changed, 'custom', "F j, Y, g:i a"); ?></td>
+    </tr>
+    <tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
+      <th>Template Name</th>
+      <td><?php print $node->template->name; ?></td>
+    </tr>
+    <tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
+      <th>Data File</th>
+      <td><?php print $node->file;?></td>
+    </tr>
+    <tr class="tripal_bulk_loader-table-odd-row tripal-table-odd-row">
+      <th>Job Status</th>
+      <td><?php print $node->job_status;?></td>
+    </tr>
+    <?php if (isset($node->job)) { if (isset($node->job->progress)) { ?>
+    <tr class="tripal_bulk_loader-table-even-row tripal-table-even-row">
+      <th>Job Progress</th>
+      <td><?php print $node->job->progress . '% (' . l('view job', 'admin/tripal/tripal_jobs/view/' . $node->job_id) . ')';?></td>
+    </tr>
+    <?php }} ?>
+  </table>
 </div>
 
 <?php if (!$teaser) { ?>

tripal_bulk_loader/theme/tripal_bulk_loader_template.tpl.php

@@ -10,29 +10,29 @@
   $template->template_array = unserialize($template->template_array);
 
   // Summarize Template
-	$fields = array();
-	$constants = array();
-	foreach ($template->template_array as $priority => $table_array) {
-		if (!is_array($table_array)) {
-			continue;
-		}
+  $fields = array();
+  $constants = array();
+  foreach ($template->template_array as $priority => $table_array) {
+    if (!is_array($table_array)) {
+      continue;
+    }
 
-		$table = $table_array['table'];
-		$record = $table_array['record_id'];
-		foreach ($table_array['fields'] as $field) {
-			if (preg_match('/table field/', $field['type'])) {
-				$field['table'] = $table;
-				$field['record'] = $record;
-				$sheet = 0;//$field['spreadsheet sheet'];
-				$column = $field['spreadsheet column'];
-				$fields[$sheet.'-'.$column][] = $field;
-			} elseif ($field['type'] == 'constant') {
-				$field['table'] = $table;
-				$field['record'] = $record;
-				$constants[] = $field;
-			}
-		}
-	}
+    $table = $table_array['table'];
+    $record = $table_array['record_id'];
+    foreach ($table_array['fields'] as $field) {
+      if (preg_match('/table field/', $field['type'])) {
+        $field['table'] = $table;
+        $field['record'] = $record;
+        $sheet = 0;//$field['spreadsheet sheet'];
+        $column = $field['spreadsheet column'];
+        $fields[$sheet.'-'.$column][] = $field;
+      } elseif ($field['type'] == 'constant') {
+        $field['table'] = $table;
+        $field['record'] = $record;
+        $constants[] = $field;
+      }
+    }
+  }
 ?>
 
 <div id="tripal_bulk_loader-base-box" class="tripal_bulk_loader-info-box tripal-info-box">
@@ -47,7 +47,7 @@
     <?php $row = 'even' ?>
     <?php foreach ($constants as $field) {?>
       <tr class="tripal_bulk_loader-table-<?php print $row; ?>-row tripal-table-<?php print $row; ?>-row">
-				<td><?php print $field['record'];?></td>
+        <td><?php print $field['record'];?></td>
         <td><?php print $field['title'];?></td>
         <td><?php print $field['constant value']; ?></td>
         <td><?php print $field['table'];?></td>
@@ -66,7 +66,7 @@
   <?php foreach ($fields as $column) {?>
     <?php foreach ($column as $field) {?>
     <tr class="tripal_bulk_loader-table-<?php print $row; ?>-row tripal-table-<?php print $row; ?>-row">
-    	<td><?php print $field['record'];?></td>
+      <td><?php print $field['record'];?></td>
       <td><?php print $field['title'];?></td>
       <td><?php print $field['spreadsheet column'];?></td>
       <td><?php print $field['table'];?></td>

tripal_contact/includes/tripal_contact.chado_node.inc

@@ -549,27 +549,27 @@ function chado_contact_delete(&$node) {
  */
 function tripal_contact_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
-  	case 'chado_contact':
-  	  // Show feature browser and counts
-  	  if ($view_mode == 'full') {
-  	    $node->content['tripal_contact_base'] = array(
-  	      '#value' => theme('tripal_contact_base', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_contact_properties'] = array(
-  	      '#value' => theme('tripal_contact_properties', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_contact_publications'] = array(
-  	      '#value' => theme('tripal_contact_publications', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_contact_relationships'] = array(
-  	      '#value' => theme('tripal_contact_relationships', array('node' => $node)),
-  	    );
-  	  }
-  	  if ($view_mode == 'teaser') {
-  	    $node->content['tripal_contact_teaser'] = array(
-  	      '#value' => theme('tripal_contact_teaser', array('node' => $node)),
-  	    );
-  	  }
-  	  break;
+    case 'chado_contact':
+      // Show feature browser and counts
+      if ($view_mode == 'full') {
+        $node->content['tripal_contact_base'] = array(
+          '#value' => theme('tripal_contact_base', array('node' => $node)),
+        );
+        $node->content['tripal_contact_properties'] = array(
+          '#value' => theme('tripal_contact_properties', array('node' => $node)),
+        );
+        $node->content['tripal_contact_publications'] = array(
+          '#value' => theme('tripal_contact_publications', array('node' => $node)),
+        );
+        $node->content['tripal_contact_relationships'] = array(
+          '#value' => theme('tripal_contact_relationships', array('node' => $node)),
+        );
+      }
+      if ($view_mode == 'teaser') {
+        $node->content['tripal_contact_teaser'] = array(
+          '#value' => theme('tripal_contact_teaser', array('node' => $node)),
+        );
+      }
+      break;
   }
 }

tripal_contact/tripal_contact.install

@@ -48,7 +48,7 @@ function tripal_contact_requirements($phase) {
  */
 function tripal_contact_install() {
 
-	// create the module's data directory
+  // create the module's data directory
   tripal_create_moddir('tripal_contact');
 
   // add the contactprop table to Chado

tripal_contact/tripal_contact.module

@@ -62,7 +62,7 @@ function tripal_contact_menu() {
     'title' => 'Contacts',
     'description' => ('Model persons, institutes, groups, organizations, etc.'),
     'page callback' => 'tripal_contact_admin_contact_view',
-    'access arguments' => array('administer tripal contacts'),
+    'access arguments' => array('administer tripal contact'),
     'type' => MENU_NORMAL_ITEM
   );
 
@@ -81,7 +81,7 @@ function tripal_contact_menu() {
     'description' => ('Help with the contact module.'),
     'page callback' => 'theme',
     'page arguments' => array('tripal_contact_help'),
-    'access arguments' => array('administer tripal contacts'),
+    'access arguments' => array('administer tripal contact'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
@@ -91,7 +91,7 @@ function tripal_contact_menu() {
     'description' => 'Sync contacts in Chado with Drupal',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_contact_sync_form'),
-    'access arguments' => array('administer tripal contacts'),
+    'access arguments' => array('administer tripal contact'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
@@ -106,24 +106,6 @@ function tripal_contact_menu() {
     'weight' => 2
   );
 
-  // AJAX calls for adding/removing properties to a contact
-  $items['tripal_contact/properties/add'] = array(
-    'page callback' => 'tripal_contact_property_add',
-    'access arguments' => array('edit chado_contact content'),
-    'type ' => MENU_CALLBACK,
-  );
-  $items['tripal_contact/properties/description'] = array(
-    'page callback' => 'tripal_contact_property_get_description',
-    'access arguments' => array('edit chado_contact content'),
-    'type ' => MENU_CALLBACK,
-  );
-  $items['tripal_contact/properties/minus/%/%'] = array(
-    'page callback' => 'tripal_contact_property_delete',
-    'page arguments' => array(3, 4),
-    'access arguments' => array('edit chado_contact content'),
-    'type ' => MENU_CALLBACK,
-  );
-
   return $items;
 }
 

tripal_core/api/tripal_core.chado_general.api.inc

@@ -246,3 +246,29 @@ function tripal_core_get_max_chado_rank($tablename, $where_options) {
   }
 
 }
+
+/**
+ * Use this function to encapsulate text intended to be 
+ * visible only by the site administrator. A small tripal logo
+ * appears alongside the text.  Do not call this function directly, but
+ * rather, use the theme() function:
+ * 
+ *   theme('tripal_admin_message', array('message' => $my_message));
+ * 
+ * @param $message
+ *   The message to be displayed to the site administrator
+ * 
+ * @ingroup tripal_chado_api
+ */
+function theme_tripal_admin_message($variables) {
+  
+  $message = $variables['message'];
+  
+  if (!user_access('access administration pages')) {
+    return ''; 
+  }
+  return "
+    <div class=\"tripal-site-admin-only\">
+      <div class=\"tripal-site-admin-message\">$message</div>
+    </div>";
+}

tripal_core/api/tripal_core.chado_nodes.api.inc

@@ -565,7 +565,7 @@ function tripal_core_chado_node_sync_records($base_table, $max_sync = FALSE, $or
         $new_node->type = 'chado_' . $base_table;
         $new_node->uid = $user->uid;
         $new_node->{$base_table_id} = $record->{$base_table_id};
-        $new_node->library = $record;
+        $new_node->$base_table = $record;
 
         // TODO: should we get rid of this hook and use hook_node_presave() instead?
         // allow base module to set additional fields as needed

tripal_core/theme/css/tripal.css

@@ -1,150 +1,146 @@
-.tripal-info-box {
-   width: 100%;
-   padding-bottom: 10px;
-}
-
-.tripal-info-box-nosidebar {
-   width: 100%;
-   padding-bottom: 10px;
-}
-
-.tripal-info-box-title {
-  font-size: 1.5em;
-  padding-bottom: 15px;
-}
-
-.tripal-info-box-title-nosidebar {
-  font-size: 1.5em;
-  padding-bottom: 15px;
-}
-
-.tripal-info-box-desc {
-  /* padding-bottom: 15px; */
-}
-/* hide the title when inside of a block on a panel */
-.pane-block .tripal-info-box-title {
-   visibility: hidden;
-   padding: 0;
-   margin: 0;
-   height: 0px;
-}
-
-/* no results message */
-.tripal-no-results {
-   font-style: italic;
-   padding: 10px;
-   background-color: #FFEEEE;
-}
 /**
- * Tripal Contents container: contains both the details 
- * section and the resources sidebar
+ * The Tripal generic node template (node--chado-generc.tpl.php)
+ * has an outer div box with class 'tripal-contents' and with an inner 
+ * table with an id of 'tripal-contents-table'.  The table has a single
+ * row with two columns.  The smaller left column houses the table of 
+ * contents (TOC) for the node data.  The larger right column houses the data:
+ *
+ * |-----------------------------------------------|
+ * |  .tripal-contents                             |
+ * | |-------------------------------------------| |
+ * | | #tripal-contents-table                    | |
+ * | |        |                                  | |
+ * | |        |                                  | |
+ * | | TOC    |          Data                    | |
+ * | | column |          Column                  | |
+ * | |        |                                  | |
+ * | |        |                                  | |
+ * | |        |                                  | |
+ * | |-------------------------------------------| |
+ * |-----------------------------------------------|
+ *
+ * The tripal-contents box and the inner table are designed to fill the width
+ * of the contents section of any theme.  Customize the CSS below to change
+ * the look-and-feel.
+ *
  */
-.tripal_contents {
+
+.tripal-contents {
   width: 100%;
-  position: relative;
 }
 
-#tripal_contents_table {
+#tripal-contents_table {
   padding: 0px !important;
-  margin: 0px !important;
-  
+  margin:  0px !important;
 }
 
-#tripal_contents_table tbody {
+/**
+ * The table formatting must override the default theme.  This is because
+ * the table is meant for organizing the sidebar and contents so they don't
+ * slip and slide around as would happen with div boxes that were floated.
+ * Therefore, we use !important to keep the default theme from overrideing
+ * the table settings. 
+ */
+ 
+#tripal-contents-table tbody {
   padding: 0px !important;
-  margin: 0px !important;
-  border: 0px solid #FFFFFF;
+  margin:  0px !important;
+  border:  none !important;
+  background-color: transparent !important;
 }
-
-.tripal_contents_table_td { 
-  border: 0px solid #FFFFFF !important;
+.tripal-contents-table-tr {
   padding: 0px !important;
-  text-align: left;
-  vertical-align: top;
-}
-.tripal_contents_table_tr {
-background-color: transparent;
+  margin:  0px !important;
+  border:  none !important;
+  background-color: transparent !important;
+}
+.tripal-contents-table-td-toc { 
+  border: 1px solid #888888 !important;
+  margin:  0px !important;
+  padding: 10px !important;
+  background-color: transparent !important;
+  text-align: left !important;
+  vertical-align: top !important;
+}
+.tripal-contents-table-td-data { 
+  border: none !important;
+  margin:  0px !important;
+  padding: 0px 0px 0px 20px !important;
+  background-color: transparent !important;
+  text-align: left !important;
+  vertical-align: top !important;
 }
 
 /**
- * Resources Sidebar
+ * The table of contents is an unordered list. The following can are used
+ * to style the list 
  */
-.tripal_toc {
-  padding: 0px; 
-  margin-right: 0px;
-}
-.tripal_toc ul {
-  margin: 0 !important;
-  padding: 0 !important;
-  list-style-type: none;
-}
-.tripal_toc li {
-	background-color: #EEEEEE;
-  border-style:solid;
-  border-width:1px;
-  border-color: #999999;
-  padding: 3px 20px 3px 20px;
-  margin: 2px 0 2px 0;
-}
-.tripal_toc_title {
-  font-size: 1.5em;
-  line-height: 110%;
-  padding-bottom: 10px;
-}
-.tripal_toc_desc {
+.tripal_toc_list ul {
+
 }
-/**
- * Details Section
- */
-.tripal_details {
-  padding: 0px 20px 20px 20px;
-  min-height: 500px;
-  margin-right: 10px;
-  margin-bottom: 10px;
-  overflow:auto;
+.tripal_toc_list li {
+  padding: 3px 20px 3px 10px !important;
+  margin: 2px 0 2px 0 !important;
 }
 
-.tripal_details_full {
-  float: left;
-  background-color: #FFFFFF;
-
-  -moz-border-radius: 15px;
-  -webkit-border-radius: 15px;
-  -khtml-border-radius: 15px;
-  border-radius: 15px;
-
-  -moz-box-shadow: 3px 3px 4px #888888;
-  -webkit-box-shadow: 3px 3px 4px #888888;
-  box-shadow: 3px 3px 4px #888888;
-  padding: 20px;
-  min-height: 500px;
-  margin-right: 10px;
-  margin-bottom: 10px;
-  border-style:solid;
-  border-width:1px;
-  
-  overflow:auto;
-}
-/**
- * Tables
+/******************************************************************************
+ * The links that appear in the TOC section are added dynamically by
+ * JavaScript code found at the top of the node--chado-generc.tpl.php template.
+ * Each link in the TOC cooresponds to a "block" of data added to the Data
+ * Column. Initially, the JavaScript hids all "blocks" except for the "Details"
+ * block.  There will be as many blocks as there are TOC links.
+ *
+ * By default, all blocks have the following layout that consists of a 
+ * container div box with the class 'tripal-info-box', a div box to house the
+ * block title with the class 'tripal-info-box-title', and a div box to
+ * house a brief description about the block with the class 
+ * 'tripal-info-box-desc' 
+ *
+ * |-----------------------------------------------|
+ * |  .tripal-info-box                             |
+ * | |-------------------------------------------| |
+ * | | .tripal-info-box-title                    | |
+ * | |-------------------------------------------| |
+ * | | .tripal-info-box-desc                     | |
+ * | |-------------------------------------------| |
+ * |                                               |
+ * | (Block data goes here)                        |
+ * |                                               |
+ * |                                               |
+ * |                                               |
+ * |                                               |
+ * |-----------------------------------------------|
  */
-.tripal-subtable {
-  border-collapse:collapse;
-  border: 0px solid black;
-  width: auto;
+.tripal-info-box {
+   width: 100%;
+   padding-bottom: 10px;
 }
 
-.tripal-subtable td {
-  padding: 0px 5px 5px 0px; 
-  border: 0px solid black;
+.tripal-info-box-title {
+  font-size: 1.5em;
+  padding-bottom: 15px;
 }
 
-.tripal-notice {
-  color: red;
+.tripal-info-box-desc {
+
 }
 
-/**
- * Teaser
+/******************************************************************************
+ * The teaser appears anywhere that a small snippet of the content is required.
+ * When any node in Drupal is published to the home page a teaser is used.
+ * Teasers can also be used in views to provide lists of content. The 
+ * teaser template is similar to the block but with the following sections and
+ * classes
+ *
+ * |-----------------------------------------------|
+ * |  .tripal-teaser                               |
+ * | |-------------------------------------------| |
+ * | | .tripal-teaser-title                      | |
+ * | |-------------------------------------------| |
+ * | | .tripal-teaser-text                       | |
+ * | |                                           | |
+ * | |-------------------------------------------| |
+ * |-----------------------------------------------|
  */
 .tripal-teaser {
   clear_both;
@@ -158,9 +154,35 @@ background-color: transparent;
   text-align: justify;
   text-justify:inter-word;
 }
+
+/**
+ * some nodes such as the organism node may have images. This class
+ * is used to format any image that appears in the teaser 
+ */
 .tripal-teaser-img {
   width: 100px; 
   float: left; 
   padding-right: 10px; 
   padding-bottom: 5px;
 }
+
+/******************************************************************************
+ * Administrative CSS classes
+ *****************************************************************************/
+ 
+ /**
+  * This class is used when providing hints or other instructions to the 
+  * site administrator
+  */ 
+ 
+.tripal-site-admin-only {
+   background-image: url("../images/TripalLogo-sm.png");
+   background-repeat: no-repeat;
+   background-color: #BBBBFF;
+}
+
+.tripal-site-admin-message {
+   padding: 10px 10px 10px 55px;
+   font-style: italic;
+}
+

tripal_core/theme/node--chado-generic.tpl.php

@@ -23,17 +23,8 @@ else { ?>
 <script type="text/javascript">
 (function ($) {
   Drupal.behaviors.<?php print $ttype?>Behavior = {
-    attach: function (context, settings){ <?php
-      // hide the resource sidbar if requested and strech the details section
-      if ($no_sidebar) { ?>    
-        $(".tripal_toc").hide();
-        $(".tripal_details").addClass("tripal_details_full");
-        $(".tripal_details_full").removeClass("tripal_details"); <?php
-      } 
-      // use default resource sidebar
-      else { ?>        
-        $(".tripal-info-box").hide(); <?php
-      } ?>
+    attach: function (context, settings){ 
+      $(".tripal-info-box").hide();
  
       // iterate through all of the info boxes and add their titles
       // to the table of contents
@@ -79,49 +70,51 @@ else { ?>
 })(jQuery);
 </script>
 
-<div id="tripal_<?php print $ttype?>_content" class="tripal_contents">
-  <table id="tripal_contents_table">
-    <tr class="tripal_contents_table_tr">
-      <td nowrap class="tripal_contents_table_td"  align="left">
-        <div id="tripal_<?php print $ttype?>_toc" class="tripal_toc">
-          <ul id="tripal_<?php print $ttype?>_toc_list" class="tripal_toc_list">
-          
-           <!-- Resource Links CCK elements --><?php
-           if(property_exists($node, 'field_resource_links')) {
-             for($i = 0; $i < count($node->field_resource_links); $i++){
-               if($node->field_resource_links[$i]['value']){
-                 $matches = preg_split("/\|/",$node->field_resource_links[$i]['value']);?>
-                 <li><a href="<?php print $matches[1] ?>" target="_blank"><?php print $matches[0] ?></a></li><?php
-               }
+<div id="tripal_<?php print $ttype?>_content" class="tripal-contents"> <?php 
+  if ($page['tripal_sidebar']) { ?>
+    <div id="tripal-sidebar" class="column sidebar">
+      <div class="section">
+        <?php print render($page["chado_" . $ttype . " _toc"]); ?>
+      </div>
+    </div><?php 
+  } ?>
+  <table id="tripal-contents-table">
+    <tr class="tripal-contents-table-tr">
+      <td nowrap class="tripal-contents-table-td tripal-contents-table-td-toc"  align="left">
+        <ul id="tripal_<?php print $ttype?>_toc_list" class="tripal_toc_list">
+        
+         <!-- Resource Links CCK elements --><?php
+         if(property_exists($node, 'field_resource_links')) {
+           for($i = 0; $i < count($node->field_resource_links); $i++){
+             if($node->field_resource_links[$i]['value']){
+               $matches = preg_split("/\|/",$node->field_resource_links[$i]['value']);?>
+               <li><a href="<?php print $matches[1] ?>" target="_blank"><?php print $matches[0] ?></a></li><?php
              }
            }
-           ?> 
-            </ul>
-          </div>
+         }
+         ?> 
+          </ul>
         </td>
-        <td class="tripal_contents_table_td" align="left" width="100%">
-          <div id="tripal_<?php print $ttype?>_details" class="tripal_details">
-        
-           <!-- Resource Blocks CCK elements --> <?php
-           if (property_exists($node, 'field_resource_titles')) {
-             for ($i = 0; $i < count($node->field_resource_titles); $i++){
-               if ($node->field_resource_titles[$i]['value']){ ?>
-                 <div id="tripal_<?php print $ttype?>-resource_<?php print $i?>-box" class="tripal_<?php print $ttype?>-info-box tripal-info-box">
-                   <div class="tripal_<?php print $ttype?>-info-box-title tripal-info-box-title"><?php print $node->field_resource_titles[$i]['value'] ?></div>
-                   <?php print $node->field_resource_blocks[$i]['value']; ?>
-                 </div> <?php
-               }
-             } 
-           }?>
-           <!-- Let modules add more content -->
-           <?php
-             foreach ($content as $key => $values) {
-               if (array_key_exists('#value', $values)) {
-                 print $content[$key]['#value'];
-               }
+        <td class="tripal-contents-table-td-data" align="left" width="100%">
+         <!-- Resource Blocks CCK elements --> <?php
+         if (property_exists($node, 'field_resource_titles')) {
+           for ($i = 0; $i < count($node->field_resource_titles); $i++){
+             if ($node->field_resource_titles[$i]['value']){ ?>
+               <div id="tripal_<?php print $ttype?>-resource_<?php print $i?>-box" class="tripal_<?php print $ttype?>-info-box tripal-info-box">
+                 <div class="tripal_<?php print $ttype?>-info-box-title tripal-info-box-title"><?php print $node->field_resource_titles[$i]['value'] ?></div>
+                 <?php print $node->field_resource_blocks[$i]['value']; ?>
+               </div> <?php
              }
-           ?>
-        </div>
+           } 
+         }?>
+         <!-- Let modules add more content -->
+         <?php
+           foreach ($content as $key => $values) {
+             if (array_key_exists('#value', $values)) {
+               print $content[$key]['#value'];
+             }
+           }
+         ?>
       </td>
     </tr>
   </table>

tripal_core/tripal_core.module

@@ -150,7 +150,7 @@ function tripal_core_menu() {
     'description' => "Manage the behavior or Tripal and its various modules.",
     'weight' => -8,
     'page callback' => 'system_admin_menu_block_page',
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal'),
     'file' => 'system.admin.inc',
     'file path' => drupal_get_path('module', 'system'),
   );
@@ -158,26 +158,26 @@ function tripal_core_menu() {
     'title' => 'Chado Schema',
     'description' => "Tools to extend the chado schema through custom tables & materialized views.",
     'weight' => -2,
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal'),
   );
   $items['admin/tripal/chado'] = array(
     'title' => 'Chado Modules',
     'description' => 'Configuration for specific chado data types such as Vocabularies, Features, etc.',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -6
   );
   $items['admin/tripal/loaders'] = array(
     'title' => 'Chado Data Loaders',
     'description' => 'Tools facilitating loading data into the chado database. Includes a generic tab-delimited loader (Bulk Loader).',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -4
   );
   $items['admin/tripal/extension'] = array(
     'title' => 'Extension Modules',
     'description' => 'Configuration for Tripal extension modules.',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => 0
   );
@@ -186,7 +186,7 @@ function tripal_core_menu() {
   $items['admin/tripal/setup'] = array(
     'title' => 'Setup Tripal',
     'description' => 'Tools for initial setup of Tripal',
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal'),
     'weight' => -8
   );
   $items['admin/tripal/setup/customize'] = array(
@@ -194,7 +194,7 @@ function tripal_core_menu() {
     'description' => 'Information on how to customize tripal',
     'page callback' => 'theme',
     'page arguments' => array('tripal_core_customize'),
-    'access arguments' => array('administer site configuration'),
+    'access arguments' => array('administer tripal'),
     'weight' => 10
   );
   $items['admin/tripal/setup/chado_install'] = array(
@@ -212,7 +212,7 @@ function tripal_core_menu() {
     'title' => 'Jobs',
     'description' => 'Jobs managed by Tripal',
     'page callback' => 'tripal_jobs_admin_view',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
@@ -221,7 +221,7 @@ function tripal_core_menu() {
     'description' => 'Help for the tripal job management system',
     'page callback' => 'theme',
     'page arguments' => array('tripal_core_job_help'),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
@@ -230,7 +230,7 @@ function tripal_core_menu() {
     'description' => 'Cancel a pending job',
     'page callback' => 'tripal_jobs_cancel',
     'page arguments' => array(4),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_jobs/rerun/%'] = array(
@@ -238,7 +238,7 @@ function tripal_core_menu() {
     'description' => 'Re-run an existing job.',
     'page callback' => 'tripal_jobs_rerun',
     'page arguments' => array(4),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_jobs/view/%'] = array(
@@ -246,14 +246,14 @@ function tripal_core_menu() {
     'description' => 'View job details.',
     'page callback' => 'tripal_jobs_view',
     'page arguments' => array(4),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/tripal_jobs/views/jobs/enable'] = array(
     'title' => 'Enable Jobs Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
     'page arguments' => array('tripal_core_admin_jobs', 'admin/tripal/tripal_jobs'),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
 
@@ -262,7 +262,7 @@ function tripal_core_menu() {
     'title' => 'Materialized Views',
     'description' => 'Materialized views are used to improve speed of large or complex queries.',
     'page callback' => 'tripal_mview_admin_view',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
@@ -271,7 +271,7 @@ function tripal_core_menu() {
     'description' => 'Help for the materialized views management system',
     'page callback' => 'theme',
     'page arguments' => array('tripal_core_mviews_help'),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
@@ -280,7 +280,7 @@ function tripal_core_menu() {
     'title' => 'List Materialized Views',
     'description' => 'A list of existing materialized views with the ability to edit & delete existing materialized views.',
     'page callback' => 'tripal_mviews_report',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
@@ -290,7 +290,7 @@ function tripal_core_menu() {
     'description' => 'Materialized views are used to improve speed of large or complex queries. These are database views as compared to Drupal views.',
     'page callback' => 'tripal_mview_report',
     'page arguments' => array(5),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/schema/mviews/new'] = array(
@@ -298,14 +298,14 @@ function tripal_core_menu() {
     'description' => 'Create a new materialized view.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_mviews_form'),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/schema/mviews/edit/%'] = array(
     'title' => 'Edit Materialized View',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_mviews_form', 5),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/schema/mviews/action/%/%'] = array(
@@ -313,7 +313,7 @@ function tripal_core_menu() {
     'description' => 'Materialized views are used to improve speed of large or complex queries.',
     'page callback' => 'tripal_mviews_action',
     'page arguments' => array(5, 6, "1"),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
 
@@ -322,7 +322,7 @@ function tripal_core_menu() {
     'title' => 'Custom Tables',
     'description' => 'Creation of custom tables that are added to Chado database.',
     'page callback' => 'tripal_custom_table_admin_view',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
@@ -331,7 +331,7 @@ function tripal_core_menu() {
     'description' => 'Help for the tripal job management system',
     'page callback' => 'theme',
     'page arguments' => array('tripal_core_job_help'),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
@@ -340,7 +340,7 @@ function tripal_core_menu() {
     'title' => 'List of Custom Tables',
     'description' => 'Provides a list of all custom tables created by Tripal and allows for editing or removing existing custom tables.',
     'page callback' => 'tripal_custom_tables_list',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_NORMAL_ITEM,
     'weight' => -10
   );
@@ -350,21 +350,21 @@ function tripal_core_menu() {
     'description' => 'Custom tables are added to Chado.',
     'page callback' => 'tripal_custom_table_view',
     'page arguments' => array(4),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/schema/custom_tables/new'] = array(
     'title' => 'Create Custom Table',
     'description' => 'An interface for creating your own custom tables.',
     'page callback' => 'tripal_custom_table_new_page',
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/schema/custom_tables/edit/%'] = array(
     'title' => 'Edit Custom Table',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_custom_tables_form', 4),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/schema/custom_tables/action/%/%'] = array(
@@ -372,14 +372,14 @@ function tripal_core_menu() {
     'description' => 'Custom tables are added to Chado.',
     'page callback' => 'tripal_custom_tables_action',
     'page arguments' => array(4, 5, "1"),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/schema/custom_tables/views/tables/enable'] = array(
     'title' => 'Enable Custom Tables Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
     'page arguments' => array('tripal_core_admin_custom_table', 'admin/tripal/schema/custom_tables'),
-    'access arguments' => array('access administration pages'),
+    'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
 
@@ -399,6 +399,10 @@ function tripal_core_permission() {
       'title' => t('Install Chado'),
       'description' => t('Allow the user to install or upgrade a Chado database in the existing Drupal database.')
     ),
+    'administer tripal' => array(
+      'title' => t('Administer Tripal'),
+      'description' => t('Allow the user to access administrative pages of Tripal.')
+    ),
   );
 }
 
@@ -449,9 +453,17 @@ function tripal_core_theme($existing, $type, $theme, $path) {
       'function' => 'theme_chado_node_relationships_form_table',
       'render element' => 'element',
     ),
+    
+    // Admin messages theme
+    // --------------------------------
+    'tripal_admin_message' => array(
+      'function' => 'theme_tripal_admin_message',
+      'variables' => array('message' => NULL),
+    )
   );
 }
 
+
 /**
  * Implements hook_job_describe_args().
  * Describes the arguements for the tripal_update_mview job to allow for greater
@@ -520,4 +532,39 @@ function tripal_core_views_api() {
   return array(
     'api' => 3.0,
   );
+}
+
+/**
+ * After the node is built, we want to add instructions to each
+ * content section letting the administrator know which template
+ * they can customize
+ * 
+ * @param unknown $build
+ */
+function tripal_core_node_view_alter(&$build) {
+  global $theme;
+  
+
+  $cache = cache_get("theme_registry:$theme", 'cache');
+  $paths = array();
+  foreach ($build as $key => $value) {
+    if (preg_match('/^tripal_/', $key)) {
+      if (array_key_exists($key, $cache->data)) {
+        $paths[$key] = $cache->data[$key]['path'];
+      }
+    }
+  }
+  if (count($paths) > 0) {
+    $message = '<p>The content displayed on this page is provided by the following templates: <ul>';
+    foreach ($paths as $template => $path) {
+      $message .= "<li>$key: $path</li>";
+    }
+    $message .= "</ul>";
+    $build['tripal_template_paths']['#value'] = theme(
+      'theme_tripal_admin_message',
+      array('message' => $message)
+    );
+  }
+  dpm($build);
+  dpm($cache);
 }

tripal_core/tripal_launch_jobs_multi.php

@@ -99,16 +99,16 @@ function runjob($sitename, $username) {
 
   drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
 
-	// check to make sure the username is valid
-	$results = db_query("SELECT * FROM {users} WHERE name = :name", array(':name' => $username));
-	$u = $results->fetchObject();
-	if (!$u) {
-	  fwrite($stdout, "'$username' is not a valid Drupal username. exiting...\n");
-	  exit;
-	}
-	
-	global $user;
-	$user = user_load($u->uid);
+  // check to make sure the username is valid
+  $results = db_query("SELECT * FROM {users} WHERE name = :name", array(':name' => $username));
+  $u = $results->fetchObject();
+  if (!$u) {
+    fwrite($stdout, "'$username' is not a valid Drupal username. exiting...\n");
+    exit;
+  }
+  
+  global $user;
+  $user = user_load($u->uid);
 
   tripal_jobs_launch();
 }

tripal_cv/theme/js/jquery-treeview/demo/source.php

@@ -2,86 +2,86 @@
 if ($_REQUEST['root'] == "source"):
 ?>
 [
-	{
-		"text": "1. Pre Lunch (120 min)",
-		"expanded": true,
-		"classes": "important",
-		"children":
-		[
-			{
-				"text": "1.1 The State of the Powerdome (30 min)"
-			},
-		 	{
-				"text": "1.2 The Future of jQuery (30 min)"
-			},
-		 	{
-				"text": "1.2 jQuery UI - A step to richnessy (60 min)"
-			}
-		]
-	},
-	{
-		"text": "2. Lunch  (60 min)"
-	},
-	{
-		"text": "3. After Lunch  (120+ min)",
-		"children":
-		[
-			{
-				"text": "3.1 jQuery Calendar Success Story (20 min)"
-			},
-		 	{
-				"text": "3.2 jQuery and Ruby Web Frameworks (20 min)"
-			},
-		 	{
-				"text": "3.3 Hey, I Can Do That! (20 min)"
-			},
-		 	{
-				"text": "3.4 Taconite and Form (20 min)"
-			},
-		 	{
-				"text": "3.5 Server-side JavaScript with jQuery and AOLserver (20 min)"
-			},
-		 	{
-				"text": "3.6 The Onion: How to add features without adding features (20 min)",
-				"id": "36",
-				"hasChildren": true
-			},
-		 	{
-				"text": "3.7 Visualizations with JavaScript and Canvas (20 min)"
-			},
-		 	{
-				"text": "3.8 ActiveDOM (20 min)"
-			},
-		 	{
-				"text": "3.8 Growing jQuery (20 min)"
-			}
-		]
-	}
+  {
+    "text": "1. Pre Lunch (120 min)",
+    "expanded": true,
+    "classes": "important",
+    "children":
+    [
+      {
+        "text": "1.1 The State of the Powerdome (30 min)"
+      },
+       {
+        "text": "1.2 The Future of jQuery (30 min)"
+      },
+       {
+        "text": "1.2 jQuery UI - A step to richnessy (60 min)"
+      }
+    ]
+  },
+  {
+    "text": "2. Lunch  (60 min)"
+  },
+  {
+    "text": "3. After Lunch  (120+ min)",
+    "children":
+    [
+      {
+        "text": "3.1 jQuery Calendar Success Story (20 min)"
+      },
+       {
+        "text": "3.2 jQuery and Ruby Web Frameworks (20 min)"
+      },
+       {
+        "text": "3.3 Hey, I Can Do That! (20 min)"
+      },
+       {
+        "text": "3.4 Taconite and Form (20 min)"
+      },
+       {
+        "text": "3.5 Server-side JavaScript with jQuery and AOLserver (20 min)"
+      },
+       {
+        "text": "3.6 The Onion: How to add features without adding features (20 min)",
+        "id": "36",
+        "hasChildren": true
+      },
+       {
+        "text": "3.7 Visualizations with JavaScript and Canvas (20 min)"
+      },
+       {
+        "text": "3.8 ActiveDOM (20 min)"
+      },
+       {
+        "text": "3.8 Growing jQuery (20 min)"
+      }
+    ]
+  }
 ]
 <?php else: ?>
 [
-	{
-		"text": "1. Review of existing structures",
-		"expanded": true,
-		"children":
-		[
-			{
-				"text": "1.1 jQuery core"
-			},
-		 	{
-				"text": "1.2 metaplugins"
-			}
-		]
-	},
-	{
-		"text": "2. Wrapper plugins"
-	},
-	{
-		"text": "3. Summary"
-	},
-	{
-		"text": "4. Questions and answers"
-	}
-	
+  {
+    "text": "1. Review of existing structures",
+    "expanded": true,
+    "children":
+    [
+      {
+        "text": "1.1 jQuery core"
+      },
+       {
+        "text": "1.2 metaplugins"
+      }
+    ]
+  },
+  {
+    "text": "2. Wrapper plugins"
+  },
+  {
+    "text": "3. Summary"
+  },
+  {
+    "text": "4. Questions and answers"
+  }
+  
 ]
 <?php endif; ?>

tripal_cv/theme/js/jsTree/reference/_examples/1_async.php

@@ -1,29 +1,29 @@
 <?
-	// Make sure nothing is cached
-	header("Cache-Control: must-revalidate");
-	header("Cache-Control: post-check=0, pre-check=0", false);
-	header("Pragma: no-cache");
-	header("Expires: ".gmdate("D, d M Y H:i:s", mktime(date("H")-2, date("i"), date("s"), date("m"), date("d"), date("Y")))." GMT");
-	header("Last-Modified: ".gmdate("D, d M Y H:i:s")." GMT");
+  // Make sure nothing is cached
+  header("Cache-Control: must-revalidate");
+  header("Cache-Control: post-check=0, pre-check=0", false);
+  header("Pragma: no-cache");
+  header("Expires: ".gmdate("D, d M Y H:i:s", mktime(date("H")-2, date("i"), date("s"), date("m"), date("d"), date("Y")))." GMT");
+  header("Last-Modified: ".gmdate("D, d M Y H:i:s")." GMT");
 
-	// So that the loading indicator is visible
-	sleep(1);
+  // So that the loading indicator is visible
+  sleep(1);
 
-	// The id of the node being opened
-	$id = $_REQUEST["id"];
-	//echo $id;
-	if($id == "0") {
-		echo '['."\n";
-		echo "\t".'{ attributes: { id : "pjson_1" }, state: "closed", data: "Root node 1" },'."\n";
-		echo "\t".'{ attributes: { id : "pjson_5" }, data: "Root node 2" }'."\n";
-		echo ']'."\n";
-	}
-	else {
-		echo '['."\n";
-		echo "\t".'{ attributes: { id : "pjson_2" }, data: { title : "Custom icon", icon : "../media/images/ok.png" } },'."\n";
-		echo "\t".'{ attributes: { id : "pjson_3" }, data: "Child node 2" },'."\n";
-		echo "\t".'{ attributes: { id : "pjson_4" }, data: "Some other child node" }'."\n";
-		echo ']'."\n";
-	}
-	exit();
+  // The id of the node being opened
+  $id = $_REQUEST["id"];
+  //echo $id;
+  if($id == "0") {
+    echo '['."\n";
+    echo "\t".'{ attributes: { id : "pjson_1" }, state: "closed", data: "Root node 1" },'."\n";
+    echo "\t".'{ attributes: { id : "pjson_5" }, data: "Root node 2" }'."\n";
+    echo ']'."\n";
+  }
+  else {
+    echo '['."\n";
+    echo "\t".'{ attributes: { id : "pjson_2" }, data: { title : "Custom icon", icon : "../media/images/ok.png" } },'."\n";
+    echo "\t".'{ attributes: { id : "pjson_3" }, data: "Child node 2" },'."\n";
+    echo "\t".'{ attributes: { id : "pjson_4" }, data: "Some other child node" }'."\n";
+    echo ']'."\n";
+  }
+  exit();
 ?>

tripal_cv/theme/js/jsTree/reference/_examples/full/_inc/class.tree.php

@@ -1,362 +1,362 @@
 <?
 class tree {
-	// Structure table and fields
-	var $s_table	= "";
-	var $s_fields	= array(
-			"id"		=> false,
-			"parent_id"	=> false,
-			"position"	=> false,
-			"left"		=> false,
-			"right"		=> false,
-			"level"		=> false
-		);
-
-	// Additional fields (stored in format `table_name.field_name`)
-	var $d_fields	= array();
-
-	// Tree type (or types)
-	var $adjacency	= false;
-	var $nestedset	= false;
-
-	// Database
-	var $db			= false;
-
-	// Constructor
-	function __construct($tables = array()) {
-		if(!is_array($tables) || !count($tables)) return;
-		foreach($tables as $table_name => $fields) {
-			if(is_array($fields)) {
-				foreach($fields as $key => $field) {
-					switch($key) {
-						case "id":
-						case "parent_id":
-						case "position":
-						case "left":
-						case "right":
-						case "level":
-							$this->s_table = $table_name;
-							$this->s_fields[$key] = $field;
-							break;
-						default:
-							$this->d_fields[] = $table_name.".".$field;
-							break;
-					}
-				}
-			}
-		}
-
-		// Determine what kind of a tree is used (or both)
-		if($this->s_fields["id"] && $this->s_fields["position"])														$this->adjacency = true;
-		if($this->s_fields["id"] && $this->s_fields["left"] && $this->s_fields["right"] && $this->s_fields["level"])	$this->nestedset = true;
-
-		// Database
-		$this->db = new DB;
-	}
-	function tree($tables = array()) { return $this->__construct($tables); } // PHP 4 compatibilty
-
-	// WRITING FUNCTIONS
-	// Function for moving nodes
-	// ID is the node that is being moved - 0 is creating a new NODE
-	// REF_ID is the reference node in the move
-	// TYPE is one of "after", "before" or "inside"
-	function move($id, $ref_id, $type, $mode = "move") {
-		if(!in_array($type, array("after", "before", "inside"))) return false;
-
-		// Queries executed at the end
-		$sql	= array();
-
-		if(!(int)$id) $mode = "create";
-
-		if($mode == "create") {
-			// Fields and values that will be inserted
-			$fields	= array();
-			$values	= array();
-			// Inserting an ID
-			$fields[] = "`".$this->s_fields["id"]."`";
-			$values[] = "NULL";
-		}
-
-		// If the tree maintains an ID->PARENT_ID relation
-		if($this->adjacency) {
-			$this->db->query("SELECT `".$this->s_fields["parent_id"]."`, `".$this->s_fields["position"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$ref_id);
-			$this->db->nextr();
-
-			// Determine new parent and position
-			if($type == "inside") {
-				$new_parent_id = $ref_id;
-				$new_position = 1;
-			}
-			else {
-				$new_parent_id = (int)$this->db->f(0);
-				if($type == "before")	$new_position = $this->db->f(1);
-				if($type == "after")	$new_position = $this->db->f(1) + 1;
-			}
-
-			// Cleanup old parent
-			if($mode == "create") {
-				$old_parent_id	= -1;
-				$old_position	= 0;
-			}
-			else {
-				$this->db->query("SELECT `".$this->s_fields["parent_id"]."`, `".$this->s_fields["position"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$id);
-				$this->db->nextr();
-				$old_parent_id	= $this->db->f(0);
-				$old_position	= $this->db->f(1);
-			}
-
-			// A reorder was made
-			if($old_parent_id == $new_parent_id) {
-				if($new_position > $old_position) {
-					$new_position = $new_position - 1;
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$old_parent_id." AND `".$this->s_fields["position"]."` BETWEEN ".($old_position + 1)." AND ".$new_position;
-				}
-				if($new_position < $old_position) {
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` + 1 WHERE `".$this->s_fields["parent_id"]."` = ".$old_parent_id." AND `".$this->s_fields["position"]."` BETWEEN ".$new_position." AND ".($old_position - 1);
-				}
-			}
-			else {
-				// Fix old parent (move siblings up)
-				$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$old_parent_id." AND `".$this->s_fields["position"]."` > ".$old_position;
-				// Prepare new parent (move sibling down)
-				$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` + 1 WHERE `".$this->s_fields["parent_id"]."` = ".$new_parent_id." AND `".$this->s_fields["position"]."` >".($type != "after" ? "=" : "")." ".$new_position;
-			}
-			// Move the node to the new position
-			if($mode == "create") {
-				$fields[] = "`".$this->s_fields["parent_id"]."`";
-				$fields[] = "`".$this->s_fields["position"]."`";
-				$values[] = $new_parent_id;
-				$values[] = $new_position;
-			}
-			else {
-				$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = ".$new_position.", `".$this->s_fields["parent_id"]."` = ".$new_parent_id." WHERE `".$this->s_fields["id"]."` = ".(int)$id;
-			}
-		}
-
-		// If the tree maintains a nested set
-		if($this->nestedset) {
-			$this->db->query("SELECT `".$this->s_fields["id"]."` AS id, `".$this->s_fields["left"]."` AS lft, `".$this->s_fields["right"]."` AS rgt, `".$this->s_fields["level"]."` AS lvl FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` IN(".(int)$id.",".(int)$ref_id.")");
-			while($this->db->nextr()) {
-				if($id == $this->db->f("id")) {
-					$nod_lft = (int)$this->db->f("lft");
-					$nod_rgt = (int)$this->db->f("rgt");
-					$dif = $nod_rgt - $nod_lft + 1;
-				}
-				if($ref_id == $this->db->f("id")) {
-					$ref_lft = (int)$this->db->f("lft");
-					$ref_rgt = (int)$this->db->f("rgt");
-					$ref_lvl = (int)$this->db->f("lvl");
-				}
-			}
-
-			if($mode == "move") {
-				$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` - ".$dif." WHERE `".$this->s_fields["left"]."` > ".$nod_rgt;
-				$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` - ".$dif." WHERE `".$this->s_fields["right"]."` > ".$nod_rgt;
-				if($ref_lft > $nod_rgt) $ref_lft -= $dif;
-				if($ref_rgt > $nod_rgt) $ref_rgt -= $dif;
-			}
-			else $dif = 2;
-
-			$ids = array();
-			if($mode == "move") {
-				$this->db->query("SELECT `".$this->s_fields["id"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["left"]."` >= ".$nod_lft." AND `".$this->s_fields["right"]."` <= ".$nod_rgt);
-				while($this->db->nextr()) $ids[] = (int)$this->db->f(0);
-			} 
-			else $ids[] = -1;
-
-			switch($type) {
-				case "before":
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + ".$dif." WHERE `".$this->s_fields["left"]."` >= ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + ".$dif." WHERE `".$this->s_fields["right"]."` > ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
-					if($mode == "move") {
-						$dif = $ref_lft - $nod_lft;
-						$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["level"]."` = ".(int)$ref_lvl.", `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + (".$dif."), `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + (".$dif.") WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).") ";
-					}
-					else {
-						$fields[] = "`".$this->s_fields["level"]."`";
-						$fields[] = "`".$this->s_fields["left"]."`";
-						$fields[] = "`".$this->s_fields["right"]."`";
-						$values[] = (int)$ref_lvl;
-						$values[] = (int)$ref_lft;
-						$values[] = ((int)$ref_lft + 2);
-					}
-					break;
-				case "after":
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + ".$dif." WHERE `".$this->s_fields["left"]."` > ".$ref_rgt." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + ".$dif." WHERE `".$this->s_fields["right"]."` > ".$ref_rgt." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
-					if($mode == "move") {
-						$dif = ($ref_rgt + 1) - $nod_lft;
-						$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["level"]."` = ".(int)$ref_lvl.", `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + (".$dif."), `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + (".$dif.") WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).") ";
-					} else {
-						$fields[] = "`".$this->s_fields["level"]."`";
-						$fields[] = "`".$this->s_fields["left"]."`";
-						$fields[] = "`".$this->s_fields["right"]."`";
-						$values[] = (int)$ref_lvl;
-						$values[] = ((int)$ref_rgt + 1);
-						$values[] = ((int)$ref_rgt + 3);
-					}
-					break;
-				case "inside":
-				default:
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + ".$dif." WHERE `".$this->s_fields["left"]."` > ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
-					$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + ".$dif." WHERE `".$this->s_fields["right"]."` > ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
-					if($mode == "move") {
-						$dif = ($ref_lft + 1) - $nod_lft;
-						$sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["level"]."` = ".(int)($ref_lvl + 1).", `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + (".$dif."), `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + (".$dif.") WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).") ";
-					}
-					else {
-						$fields[] = "`".$this->s_fields["level"]."`";
-						$fields[] = "`".$this->s_fields["left"]."`";
-						$fields[] = "`".$this->s_fields["right"]."`";
-						$values[] = ((int)$ref_lvl + 1);
-						$values[] = ((int)$ref_lft + 1);
-						$values[] = ((int)$ref_lft + 3);
-					}
-					break;
-			}
-		}
-		
-		// If creating a new node
-		if($mode == "create") $sql[] = "INSERT INTO `".$this->s_table."` (".implode(",",$fields).") VALUES (".implode(",",$values).")";
-
-		// Applying all changes - there should be a transaction here
-		foreach($sql as $q) { $this->db->query($q); }
-
-		if($mode == "create") return mysql_insert_id();
-	}
-
-	// Function for removing nodes
-	// ID is the node (or array of nodes) that is being removed
-	function remove($id) {
-		if(is_array($id)) {
-			foreach($id as $i) { $this->remove($i); }
-			return;
-		}
-		if(!(int)$id) return false;
-
-		// Take care of nested sets (and adjacency at the same time if applicable)
-		if($this->nestedset) {
-			$this->db->query("SELECT `".$this->s_fields["left"]."` AS lft, `".$this->s_fields["right"]."` AS rgt ".( ($this->adjacency) ? " , `".$this->s_fields["parent_id"]."` AS pid, `".$this->s_fields["position"]."` AS pos " : "" )." FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$id);
-			$this->db->nextr();
-			if($this->adjacency) {
-				$pid = (int)$this->db->f("pid");
-				$pos = (int)$this->db->f("pos");
-			}
-			$lft = (int)$this->db->f("lft");
-			$rgt = (int)$this->db->f("rgt");
-			$dif = $rgt - $lft + 1;
-
-			$this->db->query("DELETE FROM `".$this->s_table."` WHERE `".$this->s_fields["left"]."` >= ".$lft." AND `".$this->s_fields["right"]."` <= ".$rgt);
-			$this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` - ".$dif." WHERE `".$this->s_fields["left"]."` > ".$rgt);
-			$this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` - ".$dif." WHERE `".$this->s_fields["right"]."` > ".$lft);
-			if($this->adjacency) {
-				$this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$pid." AND `".$this->s_fields["position"]."` > ".$pos);
-			}
-			return;
-		}
-		// Only end up here if the tree is adjacency only
-		if($this->adjacency) {
-			$this->db->query("SELECT `".$this->s_fields["parent_id"]."` AS pid, `".$this->s_fields["position"]."` AS pos FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$id);
-			$this->db->nextr();
-			$pid = (int)$this->db->f("pid");
-			$pos = (int)$this->db->f("pos");
-
-			$tmp = array($id);
-			$ids = array($id);
-			while(count($tmp)) {
-				$t = array_shift($tmp);
-				if($t) {
-					$this->db->query("SELECT `".$this->s_fields["id"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["parent_id"]."` = ".(int)$t);
-					while($this->db->nextr()) { 
-						array_push($ids, $this->db->f(0));
-						array_push($tmp, $this->db->f(0));
-					}
-				}
-			}
-			$this->db->query("DELETE FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).")");
-			$this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$pid." AND `".$this->s_fields["position"]."` > ".$pos);
-		}
-	}
-
-	function reconstruct() {
-		if(!$this->adjacency || !$this->nestedset) return;
-
-		// не знам защо да не е persistent
-		$this->db->pcn = false;
-
-		$q = "CREATE TEMPORARY TABLE temp_tree (".$this->s_fields["id"]." INTEGER NOT NULL, ".$this->s_fields["parent_id"]." INTEGER NOT NULL, ". $this->s_fields["position"]." INTEGER NOT NULL) type=HEAP";
-		$this->db->query($q);
-
-		$q = "INSERT INTO temp_tree SELECT ".$this->s_fields["id"].", ".$this->s_fields["parent_id"].", ".$this->s_fields["position"]." FROM ".$this->s_table;
-		$this->db->query($q);
-
-
-		$q = "CREATE TEMPORARY TABLE temp_stack (".$this->s_fields["id"]." INTEGER NOT NULL, ".$this->s_fields["left"]." INTEGER, ".$this->s_fields["right"]." INTEGER, ".$this->s_fields["level"]." INTEGER, stack_top INTEGER NOT NULL, ".$this->s_fields["parent_id"]." INTEGER, ".$this->s_fields["position"]." INTEGER) type=HEAP";
-		$this->db->query($q);
-		$counter = 2;
-
-		$q = "SELECT COUNT(*) as maxcounter FROM temp_tree";
-		$this->db->query($q);
-		$this->db->nextr();
-		$maxcounter = (int) $this->db->f("maxcounter") * 2;
-		$currenttop = 1;
-
-		$q = "INSERT INTO temp_stack SELECT ".$this->s_fields["id"].", 1, NULL, 0, 1, ".$this->s_fields["parent_id"].", ".$this->s_fields["position"]." FROM temp_tree WHERE ".$this->s_fields["parent_id"]." = 0";
-		$this->db->query($q);
-
-		$q = "DELETE FROM temp_tree WHERE ".$this->s_fields["parent_id"]." = 0";
-		$this->db->query($q);
-
-		while ($counter <= $maxcounter) {
-			$q = "SELECT temp_tree.".$this->s_fields["id"]." AS tempmin, temp_tree.".$this->s_fields["parent_id"]." AS pid, temp_tree.".$this->s_fields["position"]." AS lid FROM temp_stack, temp_tree WHERE temp_stack.".$this->s_fields["id"]." = temp_tree.".$this->s_fields["parent_id"]." AND temp_stack.stack_top = ".$currenttop." ORDER BY temp_tree.".$this->s_fields["position"]." ASC LIMIT 1";
-			$this->db->query($q);
-
-			if ($this->db->nextr()) {
-				$tmp = $this->db->f("tempmin");
-
-				$q = "INSERT INTO temp_stack (stack_top, ".$this->s_fields["id"].", ".$this->s_fields["left"].", ".$this->s_fields["right"].", ".$this->s_fields["level"].", ".$this->s_fields["parent_id"].", ".$this->s_fields["position"].") VALUES(".($currenttop + 1).", ".$tmp.", ".$counter.", NULL, ".$currenttop.", ".$this->db->f("pid").", ".$this->db->f("lid").")";
-				$this->db->query($q);
-				$q = "DELETE FROM temp_tree WHERE ".$this->s_fields["id"]." = ".$tmp;
-				$this->db->query($q);
-				$counter++;
-				$currenttop++;
-			}
-			else {
-				$q = "UPDATE temp_stack SET ".$this->s_fields["right"]." = ".$counter.", stack_top = -stack_top WHERE stack_top = ".$currenttop;
-				$this->db->query($q);
-				$counter++;
-				$currenttop--;
-			}
-		}
-
-		$q = "TRUNCATE TABLE ".$this->s_table;
-		$this->db->query($q);
-
-		$q = "INSERT INTO ".$this->s_table." SELECT ".$this->s_fields["id"].", ".$this->s_fields["parent_id"].", ".$this->s_fields["position"].", ".$this->s_fields["left"].", ".$this->s_fields["right"].", ".$this->s_fields["level"]." FROM temp_stack ORDER BY ".$this->s_fields["id"];
-		$this->db->query($q);
-	}
-
-	function analyze() {
-		$this->errors = array();
-		if($this->adjacency) {
-			$this->db->query("SELECT COUNT(*) FROM ".$this->s_table." s WHERE ".$this->s_fields["parent_id"]." != 0 AND (SELECT COUNT(*) FROM ".$this->s_table." WHERE ".$this->s_fields["id"]." = s.".$this->s_fields["parent_id"].") = 0 ");
-			$this->db->nextr();
-			if($this->db->f(0) > 0) $this->errors[] = "Missing parents.";
-		}
-		if($this->nestedset) {
-			$this->db->query("SELECT MAX(".$this->s_fields["right"].") FROM ".$this->s_table);
-			$this->db->nextr();
-			$n = $this->db->f(0);
-			$this->db->query("SELECT COUNT(*) FROM ".$this->s_table);
-			$this->db->nextr();
-			$c = $this->db->f(0);
-			if($n/2 != $c) $this->errors[] = "Right index does not match node count.";
-		}
-		if($this->adjacency && $this->nestedset) {
-			$this->db->query("SELECT COUNT(".$this->s_fields["id"].") FROM ".$this->s_table." s WHERE (SELECT COUNT(*) FROM ".$this->s_table." WHERE ".$this->s_fields["right"]." < s.".$this->s_fields["right"]." AND ".$this->s_fields["left"]." > s.".$this->s_fields["left"]." AND ".$this->s_fields["level"]." = s.".$this->s_fields["level"]." + 1) != (SELECT COUNT(*) FROM ".$this->s_table." WHERE ".$this->s_fields["parent_id"]." = s.".$this->s_fields["id"].") ");
-			$this->db->nextr();
-			if($this->db->f(0) > 0) $this->errors = "Adjacency and nested set do not match.";
-		}
-		return $error;
-	}
+  // Structure table and fields
+  var $s_table  = "";
+  var $s_fields  = array(
+      "id"    => false,
+      "parent_id"  => false,
+      "position"  => false,
+      "left"    => false,
+      "right"    => false,
+      "level"    => false
+    );
+
+  // Additional fields (stored in format `table_name.field_name`)
+  var $d_fields  = array();
+
+  // Tree type (or types)
+  var $adjacency  = false;
+  var $nestedset  = false;
+
+  // Database
+  var $db      = false;
+
+  // Constructor
+  function __construct($tables = array()) {
+    if(!is_array($tables) || !count($tables)) return;
+    foreach($tables as $table_name => $fields) {
+      if(is_array($fields)) {
+        foreach($fields as $key => $field) {
+          switch($key) {
+            case "id":
+            case "parent_id":
+            case "position":
+            case "left":
+            case "right":
+            case "level":
+              $this->s_table = $table_name;
+              $this->s_fields[$key] = $field;
+              break;
+            default:
+              $this->d_fields[] = $table_name.".".$field;
+              break;
+          }
+        }
+      }
+    }
+
+    // Determine what kind of a tree is used (or both)
+    if($this->s_fields["id"] && $this->s_fields["position"])                            $this->adjacency = true;
+    if($this->s_fields["id"] && $this->s_fields["left"] && $this->s_fields["right"] && $this->s_fields["level"])  $this->nestedset = true;
+
+    // Database
+    $this->db = new DB;
+  }
+  function tree($tables = array()) { return $this->__construct($tables); } // PHP 4 compatibilty
+
+  // WRITING FUNCTIONS
+  // Function for moving nodes
+  // ID is the node that is being moved - 0 is creating a new NODE
+  // REF_ID is the reference node in the move
+  // TYPE is one of "after", "before" or "inside"
+  function move($id, $ref_id, $type, $mode = "move") {
+    if(!in_array($type, array("after", "before", "inside"))) return false;
+
+    // Queries executed at the end
+    $sql  = array();
+
+    if(!(int)$id) $mode = "create";
+
+    if($mode == "create") {
+      // Fields and values that will be inserted
+      $fields  = array();
+      $values  = array();
+      // Inserting an ID
+      $fields[] = "`".$this->s_fields["id"]."`";
+      $values[] = "NULL";
+    }
+
+    // If the tree maintains an ID->PARENT_ID relation
+    if($this->adjacency) {
+      $this->db->query("SELECT `".$this->s_fields["parent_id"]."`, `".$this->s_fields["position"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$ref_id);
+      $this->db->nextr();
+
+      // Determine new parent and position
+      if($type == "inside") {
+        $new_parent_id = $ref_id;
+        $new_position = 1;
+      }
+      else {
+        $new_parent_id = (int)$this->db->f(0);
+        if($type == "before")  $new_position = $this->db->f(1);
+        if($type == "after")  $new_position = $this->db->f(1) + 1;
+      }
+
+      // Cleanup old parent
+      if($mode == "create") {
+        $old_parent_id  = -1;
+        $old_position  = 0;
+      }
+      else {
+        $this->db->query("SELECT `".$this->s_fields["parent_id"]."`, `".$this->s_fields["position"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$id);
+        $this->db->nextr();
+        $old_parent_id  = $this->db->f(0);
+        $old_position  = $this->db->f(1);
+      }
+
+      // A reorder was made
+      if($old_parent_id == $new_parent_id) {
+        if($new_position > $old_position) {
+          $new_position = $new_position - 1;
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$old_parent_id." AND `".$this->s_fields["position"]."` BETWEEN ".($old_position + 1)." AND ".$new_position;
+        }
+        if($new_position < $old_position) {
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` + 1 WHERE `".$this->s_fields["parent_id"]."` = ".$old_parent_id." AND `".$this->s_fields["position"]."` BETWEEN ".$new_position." AND ".($old_position - 1);
+        }
+      }
+      else {
+        // Fix old parent (move siblings up)
+        $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$old_parent_id." AND `".$this->s_fields["position"]."` > ".$old_position;
+        // Prepare new parent (move sibling down)
+        $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` + 1 WHERE `".$this->s_fields["parent_id"]."` = ".$new_parent_id." AND `".$this->s_fields["position"]."` >".($type != "after" ? "=" : "")." ".$new_position;
+      }
+      // Move the node to the new position
+      if($mode == "create") {
+        $fields[] = "`".$this->s_fields["parent_id"]."`";
+        $fields[] = "`".$this->s_fields["position"]."`";
+        $values[] = $new_parent_id;
+        $values[] = $new_position;
+      }
+      else {
+        $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = ".$new_position.", `".$this->s_fields["parent_id"]."` = ".$new_parent_id." WHERE `".$this->s_fields["id"]."` = ".(int)$id;
+      }
+    }
+
+    // If the tree maintains a nested set
+    if($this->nestedset) {
+      $this->db->query("SELECT `".$this->s_fields["id"]."` AS id, `".$this->s_fields["left"]."` AS lft, `".$this->s_fields["right"]."` AS rgt, `".$this->s_fields["level"]."` AS lvl FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` IN(".(int)$id.",".(int)$ref_id.")");
+      while($this->db->nextr()) {
+        if($id == $this->db->f("id")) {
+          $nod_lft = (int)$this->db->f("lft");
+          $nod_rgt = (int)$this->db->f("rgt");
+          $dif = $nod_rgt - $nod_lft + 1;
+        }
+        if($ref_id == $this->db->f("id")) {
+          $ref_lft = (int)$this->db->f("lft");
+          $ref_rgt = (int)$this->db->f("rgt");
+          $ref_lvl = (int)$this->db->f("lvl");
+        }
+      }
+
+      if($mode == "move") {
+        $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` - ".$dif." WHERE `".$this->s_fields["left"]."` > ".$nod_rgt;
+        $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` - ".$dif." WHERE `".$this->s_fields["right"]."` > ".$nod_rgt;
+        if($ref_lft > $nod_rgt) $ref_lft -= $dif;
+        if($ref_rgt > $nod_rgt) $ref_rgt -= $dif;
+      }
+      else $dif = 2;
+
+      $ids = array();
+      if($mode == "move") {
+        $this->db->query("SELECT `".$this->s_fields["id"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["left"]."` >= ".$nod_lft." AND `".$this->s_fields["right"]."` <= ".$nod_rgt);
+        while($this->db->nextr()) $ids[] = (int)$this->db->f(0);
+      } 
+      else $ids[] = -1;
+
+      switch($type) {
+        case "before":
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + ".$dif." WHERE `".$this->s_fields["left"]."` >= ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + ".$dif." WHERE `".$this->s_fields["right"]."` > ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
+          if($mode == "move") {
+            $dif = $ref_lft - $nod_lft;
+            $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["level"]."` = ".(int)$ref_lvl.", `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + (".$dif."), `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + (".$dif.") WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).") ";
+          }
+          else {
+            $fields[] = "`".$this->s_fields["level"]."`";
+            $fields[] = "`".$this->s_fields["left"]."`";
+            $fields[] = "`".$this->s_fields["right"]."`";
+            $values[] = (int)$ref_lvl;
+            $values[] = (int)$ref_lft;
+            $values[] = ((int)$ref_lft + 2);
+          }
+          break;
+        case "after":
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + ".$dif." WHERE `".$this->s_fields["left"]."` > ".$ref_rgt." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + ".$dif." WHERE `".$this->s_fields["right"]."` > ".$ref_rgt." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
+          if($mode == "move") {
+            $dif = ($ref_rgt + 1) - $nod_lft;
+            $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["level"]."` = ".(int)$ref_lvl.", `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + (".$dif."), `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + (".$dif.") WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).") ";
+          } else {
+            $fields[] = "`".$this->s_fields["level"]."`";
+            $fields[] = "`".$this->s_fields["left"]."`";
+            $fields[] = "`".$this->s_fields["right"]."`";
+            $values[] = (int)$ref_lvl;
+            $values[] = ((int)$ref_rgt + 1);
+            $values[] = ((int)$ref_rgt + 3);
+          }
+          break;
+        case "inside":
+        default:
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + ".$dif." WHERE `".$this->s_fields["left"]."` > ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
+          $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + ".$dif." WHERE `".$this->s_fields["right"]."` > ".$ref_lft." AND `".$this->s_fields["id"]."` NOT IN(".implode(",",$ids).") ";
+          if($mode == "move") {
+            $dif = ($ref_lft + 1) - $nod_lft;
+            $sql[] = "UPDATE `".$this->s_table."` SET `".$this->s_fields["level"]."` = ".(int)($ref_lvl + 1).", `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` + (".$dif."), `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` + (".$dif.") WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).") ";
+          }
+          else {
+            $fields[] = "`".$this->s_fields["level"]."`";
+            $fields[] = "`".$this->s_fields["left"]."`";
+            $fields[] = "`".$this->s_fields["right"]."`";
+            $values[] = ((int)$ref_lvl + 1);
+            $values[] = ((int)$ref_lft + 1);
+            $values[] = ((int)$ref_lft + 3);
+          }
+          break;
+      }
+    }
+    
+    // If creating a new node
+    if($mode == "create") $sql[] = "INSERT INTO `".$this->s_table."` (".implode(",",$fields).") VALUES (".implode(",",$values).")";
+
+    // Applying all changes - there should be a transaction here
+    foreach($sql as $q) { $this->db->query($q); }
+
+    if($mode == "create") return mysql_insert_id();
+  }
+
+  // Function for removing nodes
+  // ID is the node (or array of nodes) that is being removed
+  function remove($id) {
+    if(is_array($id)) {
+      foreach($id as $i) { $this->remove($i); }
+      return;
+    }
+    if(!(int)$id) return false;
+
+    // Take care of nested sets (and adjacency at the same time if applicable)
+    if($this->nestedset) {
+      $this->db->query("SELECT `".$this->s_fields["left"]."` AS lft, `".$this->s_fields["right"]."` AS rgt ".( ($this->adjacency) ? " , `".$this->s_fields["parent_id"]."` AS pid, `".$this->s_fields["position"]."` AS pos " : "" )." FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$id);
+      $this->db->nextr();
+      if($this->adjacency) {
+        $pid = (int)$this->db->f("pid");
+        $pos = (int)$this->db->f("pos");
+      }
+      $lft = (int)$this->db->f("lft");
+      $rgt = (int)$this->db->f("rgt");
+      $dif = $rgt - $lft + 1;
+
+      $this->db->query("DELETE FROM `".$this->s_table."` WHERE `".$this->s_fields["left"]."` >= ".$lft." AND `".$this->s_fields["right"]."` <= ".$rgt);
+      $this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["left"]."` = `".$this->s_fields["left"]."` - ".$dif." WHERE `".$this->s_fields["left"]."` > ".$rgt);
+      $this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["right"]."` = `".$this->s_fields["right"]."` - ".$dif." WHERE `".$this->s_fields["right"]."` > ".$lft);
+      if($this->adjacency) {
+        $this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$pid." AND `".$this->s_fields["position"]."` > ".$pos);
+      }
+      return;
+    }
+    // Only end up here if the tree is adjacency only
+    if($this->adjacency) {
+      $this->db->query("SELECT `".$this->s_fields["parent_id"]."` AS pid, `".$this->s_fields["position"]."` AS pos FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` = ".(int)$id);
+      $this->db->nextr();
+      $pid = (int)$this->db->f("pid");
+      $pos = (int)$this->db->f("pos");
+
+      $tmp = array($id);
+      $ids = array($id);
+      while(count($tmp)) {
+        $t = array_shift($tmp);
+        if($t) {
+          $this->db->query("SELECT `".$this->s_fields["id"]."` FROM `".$this->s_table."` WHERE `".$this->s_fields["parent_id"]."` = ".(int)$t);
+          while($this->db->nextr()) { 
+            array_push($ids, $this->db->f(0));
+            array_push($tmp, $this->db->f(0));
+          }
+        }
+      }
+      $this->db->query("DELETE FROM `".$this->s_table."` WHERE `".$this->s_fields["id"]."` IN (".implode(",",$ids).")");
+      $this->db->query("UPDATE `".$this->s_table."` SET `".$this->s_fields["position"]."` = `".$this->s_fields["position"]."` - 1 WHERE `".$this->s_fields["parent_id"]."` = ".$pid." AND `".$this->s_fields["position"]."` > ".$pos);
+    }
+  }
+
+  function reconstruct() {
+    if(!$this->adjacency || !$this->nestedset) return;
+
+    // не знам защо да не е persistent
+    $this->db->pcn = false;
+
+    $q = "CREATE TEMPORARY TABLE temp_tree (".$this->s_fields["id"]." INTEGER NOT NULL, ".$this->s_fields["parent_id"]." INTEGER NOT NULL, ". $this->s_fields["position"]." INTEGER NOT NULL) type=HEAP";
+    $this->db->query($q);
+
+    $q = "INSERT INTO temp_tree SELECT ".$this->s_fields["id"].", ".$this->s_fields["parent_id"].", ".$this->s_fields["position"]." FROM ".$this->s_table;
+    $this->db->query($q);
+
+
+    $q = "CREATE TEMPORARY TABLE temp_stack (".$this->s_fields["id"]." INTEGER NOT NULL, ".$this->s_fields["left"]." INTEGER, ".$this->s_fields["right"]." INTEGER, ".$this->s_fields["level"]." INTEGER, stack_top INTEGER NOT NULL, ".$this->s_fields["parent_id"]." INTEGER, ".$this->s_fields["position"]." INTEGER) type=HEAP";
+    $this->db->query($q);
+    $counter = 2;
+
+    $q = "SELECT COUNT(*) as maxcounter FROM temp_tree";
+    $this->db->query($q);
+    $this->db->nextr();
+    $maxcounter = (int) $this->db->f("maxcounter") * 2;
+    $currenttop = 1;
+
+    $q = "INSERT INTO temp_stack SELECT ".$this->s_fields["id"].", 1, NULL, 0, 1, ".$this->s_fields["parent_id"].", ".$this->s_fields["position"]." FROM temp_tree WHERE ".$this->s_fields["parent_id"]." = 0";
+    $this->db->query($q);
+
+    $q = "DELETE FROM temp_tree WHERE ".$this->s_fields["parent_id"]." = 0";
+    $this->db->query($q);
+
+    while ($counter <= $maxcounter) {
+      $q = "SELECT temp_tree.".$this->s_fields["id"]." AS tempmin, temp_tree.".$this->s_fields["parent_id"]." AS pid, temp_tree.".$this->s_fields["position"]." AS lid FROM temp_stack, temp_tree WHERE temp_stack.".$this->s_fields["id"]." = temp_tree.".$this->s_fields["parent_id"]." AND temp_stack.stack_top = ".$currenttop." ORDER BY temp_tree.".$this->s_fields["position"]." ASC LIMIT 1";
+      $this->db->query($q);
+
+      if ($this->db->nextr()) {
+        $tmp = $this->db->f("tempmin");
+
+        $q = "INSERT INTO temp_stack (stack_top, ".$this->s_fields["id"].", ".$this->s_fields["left"].", ".$this->s_fields["right"].", ".$this->s_fields["level"].", ".$this->s_fields["parent_id"].", ".$this->s_fields["position"].") VALUES(".($currenttop + 1).", ".$tmp.", ".$counter.", NULL, ".$currenttop.", ".$this->db->f("pid").", ".$this->db->f("lid").")";
+        $this->db->query($q);
+        $q = "DELETE FROM temp_tree WHERE ".$this->s_fields["id"]." = ".$tmp;
+        $this->db->query($q);
+        $counter++;
+        $currenttop++;
+      }
+      else {
+        $q = "UPDATE temp_stack SET ".$this->s_fields["right"]." = ".$counter.", stack_top = -stack_top WHERE stack_top = ".$currenttop;
+        $this->db->query($q);
+        $counter++;
+        $currenttop--;
+      }
+    }
+
+    $q = "TRUNCATE TABLE ".$this->s_table;
+    $this->db->query($q);
+
+    $q = "INSERT INTO ".$this->s_table." SELECT ".$this->s_fields["id"].", ".$this->s_fields["parent_id"].", ".$this->s_fields["position"].", ".$this->s_fields["left"].", ".$this->s_fields["right"].", ".$this->s_fields["level"]." FROM temp_stack ORDER BY ".$this->s_fields["id"];
+    $this->db->query($q);
+  }
+
+  function analyze() {
+    $this->errors = array();
+    if($this->adjacency) {
+      $this->db->query("SELECT COUNT(*) FROM ".$this->s_table." s WHERE ".$this->s_fields["parent_id"]." != 0 AND (SELECT COUNT(*) FROM ".$this->s_table." WHERE ".$this->s_fields["id"]." = s.".$this->s_fields["parent_id"].") = 0 ");
+      $this->db->nextr();
+      if($this->db->f(0) > 0) $this->errors[] = "Missing parents.";
+    }
+    if($this->nestedset) {
+      $this->db->query("SELECT MAX(".$this->s_fields["right"].") FROM ".$this->s_table);
+      $this->db->nextr();
+      $n = $this->db->f(0);
+      $this->db->query("SELECT COUNT(*) FROM ".$this->s_table);
+      $this->db->nextr();
+      $c = $this->db->f(0);
+      if($n/2 != $c) $this->errors[] = "Right index does not match node count.";
+    }
+    if($this->adjacency && $this->nestedset) {
+      $this->db->query("SELECT COUNT(".$this->s_fields["id"].") FROM ".$this->s_table." s WHERE (SELECT COUNT(*) FROM ".$this->s_table." WHERE ".$this->s_fields["right"]." < s.".$this->s_fields["right"]." AND ".$this->s_fields["left"]." > s.".$this->s_fields["left"]." AND ".$this->s_fields["level"]." = s.".$this->s_fields["level"]." + 1) != (SELECT COUNT(*) FROM ".$this->s_table." WHERE ".$this->s_fields["parent_id"]." = s.".$this->s_fields["id"].") ");
+      $this->db->nextr();
+      if($this->db->f(0) > 0) $this->errors = "Adjacency and nested set do not match.";
+    }
+    return $error;
+  }
 }
 ?>

tripal_cv/theme/js/jsTree/reference/_examples/full/_inc/database.php

@@ -1,85 +1,85 @@
 <?
-define ("server"	, $server );
-define ("db_user"	, $db_user);
-define ("db_pass"	, $db_pass);
-define ("only_db"	, $only_db);
+define ("server"  , $server );
+define ("db_user"  , $db_user);
+define ("db_pass"  , $db_pass);
+define ("only_db"  , $only_db);
 
 class DB {
-	var $srv = server;
-	var $usr = db_user;
-	var $pwd = db_pass;
-	var $odb = only_db;
-	var $pcn = false;
-	var $doe = true;
-	var $fel = true;
-	var $error_log = "mysql_errors.log";
+  var $srv = server;
+  var $usr = db_user;
+  var $pwd = db_pass;
+  var $odb = only_db;
+  var $pcn = false;
+  var $doe = true;
+  var $fel = true;
+  var $error_log = "mysql_errors.log";
 
-	function connect(){
-		if (!$this->link){
-			$this->link = ($this->pcn) ? mysql_pconnect($this->srv, $this->usr, $this->pwd) : 
-										 mysql_connect( $this->srv, $this->usr, $this->pwd) or 
-										 $this->error();
-		}
-		if (!mysql_select_db($this->odb,$this->link)) $this->error();
-		if($this->link) mysql_query("SET NAMES 'utf8'");
-		return ($this->link) ? true : false;
-	}
+  function connect(){
+    if (!$this->link){
+      $this->link = ($this->pcn) ? mysql_pconnect($this->srv, $this->usr, $this->pwd) : 
+                     mysql_connect( $this->srv, $this->usr, $this->pwd) or 
+                     $this->error();
+    }
+    if (!mysql_select_db($this->odb,$this->link)) $this->error();
+    if($this->link) mysql_query("SET NAMES 'utf8'");
+    return ($this->link) ? true : false;
+  }
 
-	function query($sql){
-		if (!$this->link && !$this->connect()) $this->error();
-		if (!($this->result = mysql_query($sql, $this->link))) $this->error($sql);
-		return ($this->result) ? true : false;
-	}
-	
-	function nextr(){
-		if (!$this->result) die ("No query pending");
-		unset($this->row);
-		$this->row = mysql_fetch_array($this->result, MYSQL_BOTH);
-		return ($this->row) ? true : false ;
-	}
+  function query($sql){
+    if (!$this->link && !$this->connect()) $this->error();
+    if (!($this->result = mysql_query($sql, $this->link))) $this->error($sql);
+    return ($this->result) ? true : false;
+  }
+  
+  function nextr(){
+    if (!$this->result) die ("No query pending");
+    unset($this->row);
+    $this->row = mysql_fetch_array($this->result, MYSQL_BOTH);
+    return ($this->row) ? true : false ;
+  }
 
-	function f($index){
-		return stripslashes($this->row[$index]);
-	}
+  function f($index){
+    return stripslashes($this->row[$index]);
+  }
 
-	function goto($row){
-		if (!$this->result) die ("No query pending");
-		if (!mysql_data_seek($this->result, $row)) $this->error();
-	}
+  function goto($row){
+    if (!$this->result) die ("No query pending");
+    if (!mysql_data_seek($this->result, $row)) $this->error();
+  }
 
-	function nf(){
-		if ($numb = mysql_num_rows($this->result) === false) $this->error();
-		return mysql_num_rows($this->result);
-	}
-	function af(){
-		return mysql_affected_rows();
-	}
-	function error($string=""){
-		echo $error = mysql_error();
-		if ($this->fel){
-			$fp = fopen($this->error_log,"a+");
-			fwrite($fp, "[".date("Y-m-d H:i:s")."]<".$error.">$string\n");
-			fclose($fp);
-		}
-		if ($this->doe){
-			if (isset($this->result)) mysql_free_result($this->result);
-			mysql_close($this->link);
-			die();
-		}
-	}
-	function insert_id(){
-		if(!$this->link) return false;
-		return mysql_insert_id();
-	}
-	function escape($string){
-		if(!$this->link) return addslashes($string);
-		return mysql_real_escape_string($string);
-	}
+  function nf(){
+    if ($numb = mysql_num_rows($this->result) === false) $this->error();
+    return mysql_num_rows($this->result);
+  }
+  function af(){
+    return mysql_affected_rows();
+  }
+  function error($string=""){
+    echo $error = mysql_error();
+    if ($this->fel){
+      $fp = fopen($this->error_log,"a+");
+      fwrite($fp, "[".date("Y-m-d H:i:s")."]<".$error.">$string\n");
+      fclose($fp);
+    }
+    if ($this->doe){
+      if (isset($this->result)) mysql_free_result($this->result);
+      mysql_close($this->link);
+      die();
+    }
+  }
+  function insert_id(){
+    if(!$this->link) return false;
+    return mysql_insert_id();
+  }
+  function escape($string){
+    if(!$this->link) return addslashes($string);
+    return mysql_real_escape_string($string);
+  }
 
-	function destroy(){
-		if (isset($this->result)) mysql_free_result($this->result);
-		if (isset($this->link_id)) mysql_close($this->link_id);
-	}
+  function destroy(){
+    if (isset($this->result)) mysql_free_result($this->result);
+    if (isset($this->link_id)) mysql_close($this->link_id);
+  }
 
 
 }

tripal_cv/theme/js/jsTree/reference/_examples/full/server.php

@@ -1,9 +1,9 @@
 <?
 // Configure database
-$server		= "localhost";
-$db_user	= "********";
-$db_pass	= "********";
-$only_db	= "********";
+$server    = "localhost";
+$db_user  = "********";
+$db_pass  = "********";
+$only_db  = "********";
 
 // Include required classes
 require_once("_inc/database.php");
@@ -20,86 +20,86 @@ while($db->nextr()) { $languages[$db->f(0)] = array($db->f(1),$db->f(2)); }
 
 // SERVER SIDE PART
 if(isset($_REQUEST["server"])) {
-	// Make sure nothing is cached
-	header("Cache-Control: must-revalidate");
-	header("Cache-Control: post-check=0, pre-check=0", false);
-	header("Pragma: no-cache");
-	header("Expires: ".gmdate("D, d M Y H:i:s", mktime(date("H")-2, date("i"), date("s"), date("m"), date("d"), date("Y")))." GMT");
-	header("Last-Modified: ".gmdate("D, d M Y H:i:s")." GMT");
+  // Make sure nothing is cached
+  header("Cache-Control: must-revalidate");
+  header("Cache-Control: post-check=0, pre-check=0", false);
+  header("Pragma: no-cache");
+  header("Expires: ".gmdate("D, d M Y H:i:s", mktime(date("H")-2, date("i"), date("s"), date("m"), date("d"), date("Y")))." GMT");
+  header("Last-Modified: ".gmdate("D, d M Y H:i:s")." GMT");
 
-	
-	switch($_REQUEST["type"]) {
-		 case "list":
-			$id = (int)str_replace("node_","",$_REQUEST["id"]);
-			$db->query("SELECT s.id, ( SELECT COUNT(*) FROM structure WHERE parent_id = s.id ) AS children, c.language, c.name FROM structure s LEFT JOIN content c ON c.id = s.id WHERE s.parent_id = ".$id." ORDER BY position");
-			$data = array();
-			$children = array();
-			while($db->nextr()) {
-				$children[$db->f("id")] = (int)$db->f("children");
-				$data[$db->f("id")][$db->f("language")] = $db->f("name");
-			}
-			echo "[\n";
-			$i = 0;
-			foreach($data as $k => $v) {
-				echo "{\n";
-				echo "\tattributes: {\n";
-				echo "\t\tid :  'node_".$k."'\n";
-				echo "\t},\n";
-				if($children[$k]) echo "\tstate: 'closed', \n";
-				echo "\tdata: {\n";
-				$kf = 0;
-				foreach($v as $lang => $name) {
-					if($kf > 0)	echo ",\n";
-					else		echo "\n";
-					$kf ++;
-					echo "\t\t'".$languages[$lang][0]."' : { title : '".$name."' }"; 
-				}
-				echo "\n";
-				echo "\t}\n";
-				echo "}";
-				if(++$i < count($data)) echo ",";
-				echo "\n";
-			}
-			echo "\n]";
-			break;
-		case "delete":
-			$id = (int)str_replace("node_","",$_REQUEST["id"]);
-			$tree->remove($id);
-			$db->query("DELETE FROM content WHERE id = ".$id);
-			echo "OK";
-			break;
+  
+  switch($_REQUEST["type"]) {
+     case "list":
+      $id = (int)str_replace("node_","",$_REQUEST["id"]);
+      $db->query("SELECT s.id, ( SELECT COUNT(*) FROM structure WHERE parent_id = s.id ) AS children, c.language, c.name FROM structure s LEFT JOIN content c ON c.id = s.id WHERE s.parent_id = ".$id." ORDER BY position");
+      $data = array();
+      $children = array();
+      while($db->nextr()) {
+        $children[$db->f("id")] = (int)$db->f("children");
+        $data[$db->f("id")][$db->f("language")] = $db->f("name");
+      }
+      echo "[\n";
+      $i = 0;
+      foreach($data as $k => $v) {
+        echo "{\n";
+        echo "\tattributes: {\n";
+        echo "\t\tid :  'node_".$k."'\n";
+        echo "\t},\n";
+        if($children[$k]) echo "\tstate: 'closed', \n";
+        echo "\tdata: {\n";
+        $kf = 0;
+        foreach($v as $lang => $name) {
+          if($kf > 0)  echo ",\n";
+          else    echo "\n";
+          $kf ++;
+          echo "\t\t'".$languages[$lang][0]."' : { title : '".$name."' }"; 
+        }
+        echo "\n";
+        echo "\t}\n";
+        echo "}";
+        if(++$i < count($data)) echo ",";
+        echo "\n";
+      }
+      echo "\n]";
+      break;
+    case "delete":
+      $id = (int)str_replace("node_","",$_REQUEST["id"]);
+      $tree->remove($id);
+      $db->query("DELETE FROM content WHERE id = ".$id);
+      echo "OK";
+      break;
 
-		case "create":
-		case "move":
-			$id		= (int)str_replace("node_","",$_REQUEST["id"]);
-			$ref_id	= (int)str_replace("node_","",$_REQUEST["ref_id"]);
-			$type	= $_REQUEST["move_type"];
-			$result = $tree->move($id,$ref_id,$type);
-			if($id == 0) {
-				foreach($languages as $k => $lang) {
-					$db->query("INSERT INTO content (id,language,name,data) VALUES(".$result.",".$k.",'New folder','')");
-				}
-				echo "node_".$result;
-			}
-			break;
-		case "rename":
-			$sql = "UPDATE content SET name = '".addslashes($_REQUEST["data"])."' WHERE id = ".(int)str_replace("node_","",$_REQUEST["id"])." AND language = ".(int)$_REQUEST["lang"];
-			$db->query($sql);
-			echo $sql;
-			break;
+    case "create":
+    case "move":
+      $id    = (int)str_replace("node_","",$_REQUEST["id"]);
+      $ref_id  = (int)str_replace("node_","",$_REQUEST["ref_id"]);
+      $type  = $_REQUEST["move_type"];
+      $result = $tree->move($id,$ref_id,$type);
+      if($id == 0) {
+        foreach($languages as $k => $lang) {
+          $db->query("INSERT INTO content (id,language,name,data) VALUES(".$result.",".$k.",'New folder','')");
+        }
+        echo "node_".$result;
+      }
+      break;
+    case "rename":
+      $sql = "UPDATE content SET name = '".addslashes($_REQUEST["data"])."' WHERE id = ".(int)str_replace("node_","",$_REQUEST["id"])." AND language = ".(int)$_REQUEST["lang"];
+      $db->query($sql);
+      echo $sql;
+      break;
 
 
-		case "loadfile":
-			$db->query("SELECT * FROM content WHERE id = ".(int)str_replace("node_","",$_REQUEST["id"])." AND language = ".(int)$_REQUEST["lang"]);
-			$db->nextr();
-			echo $db->f("data");
-			break;
-		case "savefile":
-			$sql = "UPDATE content SET data = '".addslashes($_REQUEST["data"])."' WHERE id = ".(int)str_replace("node_","",$_REQUEST["id"])." AND language = ".(int)$_REQUEST["lang"];
-			$db->query($sql);
-			echo $sql;
-			break;
-	}
-	exit();
+    case "loadfile":
+      $db->query("SELECT * FROM content WHERE id = ".(int)str_replace("node_","",$_REQUEST["id"])." AND language = ".(int)$_REQUEST["lang"]);
+      $db->nextr();
+      echo $db->f("data");
+      break;
+    case "savefile":
+      $sql = "UPDATE content SET data = '".addslashes($_REQUEST["data"])."' WHERE id = ".(int)str_replace("node_","",$_REQUEST["id"])." AND language = ".(int)$_REQUEST["lang"];
+      $db->query($sql);
+      echo $sql;
+      break;
+  }
+  exit();
 }
 ?>

tripal_cv/tripal_cv.module

@@ -158,18 +158,6 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
-
-  /*
-   * Charts
-   */
-  $items['tripal_cv_chart'] = array(
-    'path' => 'tripal_cv_chart',
-    'page callback' => 'tripal_cv_chart',
-    'page arguments' => array(1),
-    'access arguments' => array('access content'),
-    'type' => MENU_CALLBACK
-  );
-
   /*
    * Menu items for enabling views
    */
@@ -187,6 +175,18 @@ function tripal_cv_menu() {
     'access arguments' => array('administer controlled vocabularies'),
     'type' => MENU_CALLBACK,
   );
+  
+  /*
+   * Charts
+  */
+  $items['tripal_cv_chart'] = array(
+    'path' => 'tripal_cv_chart',
+    'page callback' => 'tripal_cv_chart',
+    'page arguments' => array(1),
+    'access arguments' => array('access content'),
+    'type' => MENU_CALLBACK
+  );
+  
 
   /*
    * Menu items for working with CV Trees

tripal_db/tripal_db.module

@@ -74,14 +74,14 @@ function tripal_db_menu() {
     'title' => 'Enable Database Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
     'page arguments' => array('tripal_db_admin_dbs', 'admin/tripal/chado/tripal_db'),
-    'access arguments' => array('administer controlled vocabularies'),
+    'access arguments' => array('administer db cross-references'),
     'type' => MENU_CALLBACK,
   );
   $items['admin/tripal/chado/tripal_db/views/dbxrefs/enable'] = array(
     'title' => 'Enable Reference Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
     'page arguments' => array('tripal_db_admin_dbxrefs', 'admin/tripal/chado/tripal_db'),
-    'access arguments' => array('administer controlled vocabularies'),
+    'access arguments' => array('administer db cross-references'),
     'type' => MENU_CALLBACK,
   );
 

tripal_feature/includes/tripal_feature.blocks.inc

@@ -42,6 +42,7 @@ function tripal_feature_block_info() {
 
   return $blocks;
 }
+
 /**
  *
  *
@@ -55,59 +56,59 @@ function tripal_feature_block_view($delta = '') {
 
     $block = array();
     switch ($delta) {
-    	case 'references':
-    	  $block['subject'] = t('References');
-    	  $block['content'] = theme('tripal_feature_references', $node);
-    	  break;
-    	case 'base':
-    	  $block['subject'] = t('Feature Details');
-    	  $block['content'] = theme('tripal_feature_base', $node);
-    	  break;
-    	case 'synonyms':
-    	  $block['subject'] = t('Synonyms');
-    	  $block['content'] = theme('tripal_feature_synonyms', $node);
-    	  break;
-    	case 'properties':
-    	  $block['subject'] = t('Properties');
-    	  $block['content'] = theme('tripal_feature_properties', $node);
-    	  break;
-    	case 'terms':
-    	  $block['subject'] = t('Annotated Terms');
-    	  $block['content'] = theme('tripal_feature_terms', $node);
-    	  break;
-    	case 'sequence':
-    	  $block['subject'] = t('Sequence');
-    	  $block['content'] = theme('tripal_feature_sequence', $node);
-    	  break;
-    	case 'featureloc_sequences':
-    	  $block['subject'] = t('Formatted Sequences');
-    	  $block['content'] = theme('tripal_feature_featureloc_sequences', $node);
-    	  break;
-    	case 'alignments':
-    	  $block['subject'] = t('Alignments');
-    	  $block['content'] = theme('tripal_feature_alignments', $node);
-    	  break;
-    	case 'relationships':
-    	  $block['subject'] = t('Relationships');
-    	  $block['content'] = theme('tripal_feature_relationships', $node);
-    	  break;
-    	case 'org_feature_counts':
-    	  $block['subject'] = t('Feature Type Summary');
-    	  $block['content'] = theme('tripal_organism_feature_counts', array('node' => $node));
-    	  break;
-    	case 'org_feature_browser':
-    	  $block['subject'] = t('Feature Browser');
-    	  $block['content'] = theme('tripal_organism_feature_browser', array('node' => $node));
-    	  break;
-    	case 'library_feature_browser':
-    	  $block['subject'] = t('Library Feature Browser');
-    	  $block['content'] = theme('tripal_library_feature_browser', $node);
-    	  break;
-    	case 'analysis_feature_browser':
-    	  $block['subject'] = t('Analysis Feature Browser');
-    	  $block['content'] = theme('tripal_analysis_feature_browser', $node);
-    	  break;
-    	default :
+      case 'references':
+        $block['subject'] = t('References');
+        $block['content'] = theme('tripal_feature_references', $node);
+        break;
+      case 'base':
+        $block['subject'] = t('Feature Details');
+        $block['content'] = theme('tripal_feature_base', $node);
+        break;
+      case 'synonyms':
+        $block['subject'] = t('Synonyms');
+        $block['content'] = theme('tripal_feature_synonyms', $node);
+        break;
+      case 'properties':
+        $block['subject'] = t('Properties');
+        $block['content'] = theme('tripal_feature_properties', $node);
+        break;
+      case 'terms':
+        $block['subject'] = t('Annotated Terms');
+        $block['content'] = theme('tripal_feature_terms', $node);
+        break;
+      case 'sequence':
+        $block['subject'] = t('Sequence');
+        $block['content'] = theme('tripal_feature_sequence', $node);
+        break;
+      case 'featureloc_sequences':
+        $block['subject'] = t('Formatted Sequences');
+        $block['content'] = theme('tripal_feature_featureloc_sequences', $node);
+        break;
+      case 'alignments':
+        $block['subject'] = t('Alignments');
+        $block['content'] = theme('tripal_feature_alignments', $node);
+        break;
+      case 'relationships':
+        $block['subject'] = t('Relationships');
+        $block['content'] = theme('tripal_feature_relationships', $node);
+        break;
+      case 'org_feature_counts':
+        $block['subject'] = t('Feature Type Summary');
+        $block['content'] = theme('tripal_organism_feature_counts', array('node' => $node));
+        break;
+      case 'org_feature_browser':
+        $block['subject'] = t('Feature Browser');
+        $block['content'] = theme('tripal_organism_feature_browser', array('node' => $node));
+        break;
+      case 'library_feature_browser':
+        $block['subject'] = t('Library Feature Browser');
+        $block['content'] = theme('tripal_library_feature_browser', $node);
+        break;
+      case 'analysis_feature_browser':
+        $block['subject'] = t('Analysis Feature Browser');
+        $block['content'] = theme('tripal_analysis_feature_browser', $node);
+        break;
+      default :
     }
     return $block;
   }

tripal_feature/includes/tripal_feature.chado_node.inc

@@ -630,9 +630,31 @@ function tripal_feature_node_presave($node) {
   // set the title to ensure it is always unique
   switch ($node->type) {
     case 'chado_feature':
-      $values = array('organism_id' => $node->organism_id);
+      // for a form submission the fields part of the node object
+      // but for a sync the feilds are in an object of the node
+      $name = '';
+      $uname = '';
+      $type = ''; 
+      $organism_id = null;
+      if(property_exists($node, 'feature')) {
+        $organism_id = $node->feature->organism_id;
+        $name        = $node->feature->name;
+        $uname       = $node->feature->uniquname;
+        $type_id     = $node->feature->type_id;
+        $values = array('cvterm_id' => $type_id);
+        $ftype = tripal_core_chado_select('cv', array('name'), $values);
+        $type = $ftype[0]->name;
+        
+      }
+      else {
+        $organism_id = $node->organism_id;
+        $name = $node->name;
+        $uname = $node->uniquname;
+        $type = $node->feature_type;
+      }
+      $values = array('organism_id' => $organism_id);
       $organism = tripal_core_chado_select('organism', array('genus', 'species'), $values);
-      $node->title = $node->fname . ', ' . $node->uniquename . ' (' . $node->feature_type . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
+      $node->title = $fname . ', ' . $uniquename . ' (' . $type . ') ' . $organism[0]->genus . ' ' . $organism[0]->species;
       break;
   }
 }

tripal_feature/includes/tripal_feature.seq_extract.inc

@@ -38,16 +38,12 @@ function tripal_feature_seq_extract_page() {
   // generate the search form 
   $output .= '';
   if (user_access('access administration pages')) { 
-    $output .= "
-      <div class=\"tripal-no-results\">
-        <p>Administrators, the " . l('organism_feature_count', 'admin/tripal/mviews') . " and 
-        " . l('analysis_organism', 'admin/tripal/mviews') . " materialized
+    $output .= theme('tripal_admin_message', array('message' => "
+        Administrators, the " . l('organism_feature_count', 'admin/tripal/schema/mviews') . " and 
+        " . l('analysis_organism', 'admin/tripal/schema/mviews') . " materialized
         views must be populated before using this form.  Those views should be re-populated 
-        when new data is added.  If you use the " . l('jquery_update module', 'http://drupal.org/project/jquery_update') . ", it may break this form.
-        You will need to update the  jquery_update/replace/jquery.form.js file with " .
-        l('a more recent version', 'https://raw.github.com/malsup/form/master/jquery.form.js') . "</p>         
-      </div>
-    ";
+        when new data is added."
+    ));
   }
   $output .= "<div id=\"tripal-feature-seq-extract-form-block\">";
   $output .= drupal_get_form('tripal_feature_seq_extract_form');  

tripal_feature/theme/tripal_organism/tripal_organism_feature_browser.tpl.php

@@ -73,12 +73,11 @@ if ($enabled) {
       $rows = array();
       
       // let admins know they can customize the terms that appear in the list
-      if (user_access('access administration pages')) { ?>
-         <div class="tripal-no-results">Administrators, you can specify the feature types
-         that should appear in this browser or remove it from the list of resources by navigating to the 
-         <?php print l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))) ?>.  
-         </div><?php 
-      }
+      print theme('tripal_admin_message', array('message' => "
+        Administrators, you can specify the feature types that should appear in 
+        this browser or remove it from the list of resources by navigating to the ". 
+        l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank')))
+      ));
       
       foreach ($features as $feature){
         $fname =  $feature->name;
@@ -127,36 +126,32 @@ if ($enabled) {
       print theme_pager($pager); ?>
     </div> <?php
   } 
-  else {
-    // if there are no results and this is the admin user then show some instructions
-    // otherwise nothing is shown.
-    if(user_access('access administration pages')){ ?>
-      <div id="tripal_organism-feature_browser-box" class="tripal_organism-info-box tripal-info-box">
-        <div class="tripal_organism-info-box-title tripal-info-box-title">Feature Browser</div>
-        <div class="tripal-no-results">
-          There are no features available for browsing
-          <p><br>Administrators, perform the following to show features in this browser:
-          <ul>
-            <li>Load features for this organism using the 
-            <?php print l("FASTA loader", 'admin/tripal/loaders/fasta_loader'); ?>, 
-            <?php print l("GFF Loader",   'admin/tripal/loaders/gff3_load'); ?> or 
-            <?php print l("Bulk Loader",  'admin/tripal/loaders/bulk'); ?></li>
-            <li>Sync the features that should have pages using the 
-            <?php print l("Sync features page", 'admin/tripal/chado/tripal_feature/sync');?></li>
-            <li>Return to this page to browse features.</li>
-            <li>Ensure the user 
-            <?php print l("has permission", 'admin/people/permissions'); ?> to view the feature content</li>
-          </ul> 
-          <br>
-          <br>
-          You can specify the feature types
-          that should appear in this browser or remove it from the list of resources by navigating to the 
-          <?php print l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank'))) ?>.
-          </p>
-          The feature browser will not appear to site visitors unless features are present.  These instructions only appear to site administrators.
-        </div>         
-      </div><?php
-    }
+  else {  ?>
+    <div id="tripal_organism-feature_browser-box" class="tripal_organism-info-box tripal-info-box">
+      <div class="tripal_organism-info-box-title tripal-info-box-title">Feature Browser</div>
+      <p>There are no results.</p><?php
+      print theme('tripal_admin_message', array('message' => "
+        Administrators, perform the following to show features in this browser:
+        <ul>
+          <li>Load features for this organism using the " .
+            l("FASTA loader", 'admin/tripal/loaders/fasta_loader') . ",  ".
+            l("GFF Loader",   'admin/tripal/loaders/gff3_load') . " or ".
+            l("Bulk Loader",  'admin/tripal/loaders/bulk'). "</li>
+          <li>Sync the features that should have pages using the ".
+            l("Sync features page", 'admin/tripal/chado/tripal_feature/sync'). "</li>
+          <li>Return to this page to browse features.</li>
+          <li>Ensure the user " .
+           l("has permission", 'admin/people/permissions') . " to view the feature content</li>
+        </ul>
+        <br>
+        <br>
+        You can specify the feature types
+        that should appear in this browser or remove it from the list of resources by navigating to the " . 
+        l("Tripal feature settings page", "admin/tripal/chado/tripal_feature/configuration", array('attributes' => array('target' => '_blank')))  . "
+        </p>
+        The feature browser will not appear to site visitors unless features are present. "
+      )); ?>
+    </div><?php
   }
 }
 

tripal_feature/theme/tripal_organism/tripal_organism_feature_counts.tpl.php

@@ -17,14 +17,17 @@ if ($enabled) {
       <div class="tripal_organism-info-box-title tripal-info-box-title">Data Type Summary</div>
       <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following data types are currently present for this organism</div> <?php
       // let admins know they can customize the terms that appear in the list
-      if (user_access('access administration pages')) { ?>
-         <div class="tripal-no-results">Administrators, you can customize the types of terms that appear in this report by 
-         navigating to the <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Tripal 
-         feature configuration page</a> opening the section "Feature Summary Report" and adding the list of
-         terms you want to appear in the list. You can rename terms as well.  To disable this report and 
-         remove it from the list of resources, navigate to the <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Tripal feature configuration page</a> 
-         and hide the "Feature Summary". To refresh the data,re-populate the <a href="<?php print url('admin/tripal/mviews');?>" target="_blank">organism_feature_count</a> materialized view. 
-         </div><?php 
+      if (user_access('access administration pages')) { 
+         print theme('tripal_admin_message', array('message' => "
+           Administrators, you can customize the types of terms that appear in this report by 
+           navigating to the " . l('Tripal feature configuration page', 'admin/tripal/chado/tripal_feature/configuration') . "
+           opening the section \"Feature Summary Report\" and adding the list of
+           terms you want to appear in the list. You can rename terms as well.  To disable this report and 
+           remove it from the list of resources, navigate to the " . 
+           l('Tripal feature configuration page', 'admin/tripal/tripal_feature/configuration') . "
+           and hide the \"Feature Summary\". To refresh the data,re-populate the " .
+           l('organism_feature_count', 'admin/tripal/schema/mviews') . " materialized view.")
+         ); 
       }?>
       <table id="tripal_organism-table-feature_counts" class="tripal_organism-table tripal-table tripal-table-horz">     
         <tr class="tripal_organism-table-odd-row tripal-table-even-row">
@@ -52,20 +55,19 @@ if ($enabled) {
     if (user_access('access administration pages')) { ?>
       <div id="tripal_organism-feature_counts-box" class="tripal_organism-info-box tripal-info-box">
         <div class="tripal_organism-info-box-title tripal-info-box-title">Data Type Summary</div>
-        <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following data types are currently present for this organism</div>
-        <div class="tripal-no-results">There are no features available.
-           <p><br>Administrators, to view the feature type report:
+        <div class="tripal_organism-info-box-desc tripal-info-box-desc">The following data types are currently present for this organism</div> <?php 
+        print theme('tripal_admin_message', array('message' => "
+           Administrators, to view the feature type report:
            <ul>
-              <li>Populate the <a href="<?php print url('admin/tripal/mviews');?>" target="_blank">organism_feature_count</a> materialized view</li>
+              <li>Populate the " . l('organism_feature_count', 'admin/tripal/schema/mviews') ." materialized view</li>
               <li>Refresh this page</li>
            </ul> 
-           <br><br>To disable this report and remove it from the list of resources:
+           To disable this report and remove it from the list of resources:
            <ul>
-             <li>Navigate to the <a href="<?php print url('admin/tripal/tripal_feature/configuration') ?>">Tripal feature configuration page</a> and hide the "Feature Summary"</li>
+             <li>Navigate to the " . l('Tripal feature configuration page', 'admin/tripal/chado/tripal_feature/configuration') ." and hide the \"Feature Summary\"</li>
             </ul>
-           </p>
-           This page will not appear to site visitors unless features are present. 
-         </div>
+           </p>")
+        ); ?> 
       </div><?php               
     }
   }

tripal_feature/tripal_feature.module

@@ -128,12 +128,20 @@ function tripal_feature_menu() {
     'type' => MENU_CALLBACK,
   );
 
+  // the menu link for addressing any feature (by name, uniquename, synonym)
+  $items['feature/%'] = array(
+    'page callback' => 'tripal_feature_match_features_page',
+    'page arguments' => array(1),
+    'access arguments' => array('access chado_feature content'),
+    'type' => MENU_LOCAL_TASK,
+  );
+  
   // the administative settings menu
   $items['admin/tripal/chado/tripal_feature'] = array(
     'title' => 'Features',
     'description' => 'A biological sequence or a section of a biological sequence, or a collection of such sections.',
     'page callback' => 'tripal_feature_admin_feature_view',
-    'access arguments' => array('administer tripal features'),
+    'access arguments' => array('administer tripal feature'),
     'type' => MENU_NORMAL_ITEM,
   );
 
@@ -142,7 +150,7 @@ function tripal_feature_menu() {
     'description' => 'Delete multiple features from Chado',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_delete_form'),
-    'access arguments' => array('administer tripal features'),
+    'access arguments' => array('administer tripal feature'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 2
   );
@@ -160,7 +168,7 @@ function tripal_feature_menu() {
     'description' => 'Configure the Tripal Feature module.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_admin'),
-    'access arguments' => array('administer tripal features'),
+    'access arguments' => array('administer tripal feature'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
@@ -169,7 +177,7 @@ function tripal_feature_menu() {
     'description' => 'Help with the Tripal Feature module.',
     'page callback' => 'theme',
     'page arguments' => array('tripal_feature_help'),
-    'access arguments' => array('administer tripal features'),
+    'access arguments' => array('administer tripal feature'),
     'type' => MENU_LOCAL_TASK,
     'weight' =>  10
   );
@@ -181,7 +189,7 @@ function tripal_feature_menu() {
     'description' => 'Load sequences from a multi-FASTA file into Chado',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_fasta_load_form'),
-    'access arguments' => array('administer tripal features'),
+    'access arguments' => array('administer tripal feature'),
     'type' => MENU_NORMAL_ITEM,
   );
   $items['admin/tripal/loaders/gff3_load'] = array(
@@ -189,18 +197,10 @@ function tripal_feature_menu() {
     'description' => 'Import a GFF3 file into Chado',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_feature_gff3_load_form'),
-    'access arguments' => array('administer tripal features'),
+    'access arguments' => array('administer tripal feature'),
     'type' => MENU_NORMAL_ITEM,
   );
 
-  // the menu link for addressing any feature (by name, uniquename, synonym)
-  $items['feature/%'] = array(
-    'page callback' => 'tripal_feature_match_features_page',
-    'page arguments' => array(1),
-    'access arguments' => array('access chado_feature content'),
-    'type' => MENU_LOCAL_TASK,
-  );
-
   // Enable admin view
   $items['admin/tripal/chado/tripal_feature/views/features/enable'] = array(
     'title' => 'Enable feature Administrative View',
@@ -1164,4 +1164,4 @@ function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
   if ($form_id == "chado_feature_node_form") {
     $form['actions']['preview']['#access'] = FALSE;
   }
-}
+}

tripal_featuremap/includes/tripal_featuremap.chado_node.inc

@@ -424,10 +424,15 @@ function chado_featuremap_delete(&$node) {
  * @param $node
  */
 function tripal_featuremap_node_presave($node) {
-  // if this is a chado_featuremap and the $node->featuremap object is set then we
-  // are syncing and we want to set the node title to be the same as the node name
-  if ($node->type == 'chado_featuremap' and property_exists($node, 'featuremap')) {
-    $node->title = $node->featuremap->name;
+  if ($node->type == 'chado_featuremap') {
+    // for a form submission the fields part of the node object
+    // but for a sync the feilds are in an object of the node
+    if(property_exists($node, 'featuremap')) {
+      $node->title = $node->featuremap->name;
+    }
+    else {
+      // the title is already set in the form
+    }
   }
 }
 /**
@@ -436,30 +441,30 @@ function tripal_featuremap_node_presave($node) {
  */
 function tripal_featuremap_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
-  	case 'chado_featuremap':
-  	  // Show feature browser and counts
-  	  if ($view_mode == 'full') {
-  	    $node->content['tripal_featuremap_base'] = array(
-  	      '#value' => theme('tripal_featuremap_base', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_featuremap_featurepos'] = array(
-  	      '#value' => theme('tripal_featuremap_featurepos', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_featuremap_properties'] = array(
-  	      '#value' => theme('tripal_featuremap_properties', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_featuremap_publication'] = array(
-  	      '#value' => theme('tripal_featuremap_publication', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_featuremap_references'] = array(
-  	      '#value' => theme('tripal_featuremap_references', array('node' => $node)),
-  	    );
-  	  }
-  	  if ($view_mode == 'teaser') {
-  	    $node->content['tripal_featuremap_teaser'] = array(
-  	      '#value' => theme('tripal_featuremap_teaser', array('node' => $node)),
-  	    );
-  	  }
-  	  break;
+    case 'chado_featuremap':
+      // Show feature browser and counts
+      if ($view_mode == 'full') {
+        $node->content['tripal_featuremap_base'] = array(
+          '#value' => theme('tripal_featuremap_base', array('node' => $node)),
+        );
+        $node->content['tripal_featuremap_featurepos'] = array(
+          '#value' => theme('tripal_featuremap_featurepos', array('node' => $node)),
+        );
+        $node->content['tripal_featuremap_properties'] = array(
+          '#value' => theme('tripal_featuremap_properties', array('node' => $node)),
+        );
+        $node->content['tripal_featuremap_publication'] = array(
+          '#value' => theme('tripal_featuremap_publication', array('node' => $node)),
+        );
+        $node->content['tripal_featuremap_references'] = array(
+          '#value' => theme('tripal_featuremap_references', array('node' => $node)),
+        );
+      }
+      if ($view_mode == 'teaser') {
+        $node->content['tripal_featuremap_teaser'] = array(
+          '#value' => theme('tripal_featuremap_teaser', array('node' => $node)),
+        );
+      }
+      break;
   }
 }

tripal_featuremap/tripal_featuremap.module

@@ -122,7 +122,7 @@ function tripal_featuremap_menu() {
     'description' => 'Sync featuremaps from Chado with Drupal',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_core_chado_node_sync_form', 'tripal_featuremap', 'chado_featuremap'),
-    'access arguments' => array('administer tripal featuremaps'),
+    'access arguments' => array('administer tripal featuremap'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
@@ -135,24 +135,6 @@ function tripal_featuremap_menu() {
     'type' => MENU_CALLBACK
   );
 
-  // AJAX calls for adding/removing properties to a featuremap
-  $items['tripal_featuremap/properties/add'] = array(
-    'page callback' => 'tripal_featuremap_property_add',
-    'access arguments' => array('edit chado_featuremap content'),
-    'type ' => MENU_CALLBACK,
-  );
-  $items['tripal_featuremap/properties/description'] = array(
-    'page callback' => 'tripal_featuremap_property_get_description',
-    'access arguments' => array('edit chado_featuremap content'),
-    'type ' => MENU_CALLBACK,
-  );
-  $items['tripal_featuremap/properties/minus/%/%'] = array(
-    'page callback' => 'tripal_featuremap_property_delete',
-    'page arguments' => array(3, 4),
-    'access arguments' => array('edit chado_featuremap content'),
-    'type ' => MENU_CALLBACK,
-  );
-
   $items['admin/tripal/chado/tripal_featuremap/views/featuremaps/enable'] = array(
     'title' => 'Enable featuremap Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',

tripal_genetic/tripal_genetic.module

@@ -13,6 +13,20 @@ require('theme/tripal_genetic.theme.inc');
 require('includes/tripal_genetic.schema.inc');
 require('includes/tripal_genetic.admin.inc');
 
+/**
+ *  Set the permission types that the chado module uses.  Essentially we
+ *  want permissionis 
+ *
+ * @ingroup tripal_genetic
+ */
+function tripal_genetic_permission() {
+  return array(
+    'adminster tripal genetic' => array(
+      'title' => t('Administer Genetic Module'),
+      'description' => t('Allow users to administer the genetic module.'),
+    ),
+  );
+}
 /**
  *  Menu items are automatically added for the new node types created
  *  by this module to the 'Create Content' Navigation menu item.  This function

tripal_library/includes/tripal_library.chado_node.inc

@@ -436,9 +436,17 @@ function tripal_library_node_view($node, $view_mode, $langcode) {
  * @param $node
  */
 function tripal_library_node_presave($node) {
-  // if this is a chado_library and the $node->library object is set then we
-  // are syncing and we want to set the node title to be the same as the node name
-  if ($node->type == 'chado_library' and property_exists($node, 'library')) {
-    $node->title = $node->library->name;
+  switch ($node->type) {
+    case 'chado_library':
+      // for a form submission the fields part of the node object
+      // but for a sync the feilds are in an object of the node
+      if(property_exists($node, 'library')) {
+        // set the title
+        $node->title = $node->name;
+      } 
+      else {
+        // the title field is already in the form
+      }
+      break;
   }
 }

tripal_library/tripal_library.install

@@ -154,8 +154,14 @@ function tripal_library_add_mview_library_feature_count(){
  * Adds new CV's used by this module
  */
 function tripal_library_add_cvs(){
-  tripal_cv_add_cv('library_property', 'Contains properties for libraries');
-  tripal_cv_add_cv('library_type', 'Contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).');
+  tripal_cv_add_cv(
+    'library_property', 
+    'Contains properties for libraries'
+  );
+  tripal_cv_add_cv(
+    'library_type', 
+    'Contains terms for types of libraries (e.g. BAC, cDNA, FOSMID, etc).'
+  );
 }
 /**
  * @ingroup tripal_library

tripal_library/tripal_library.module

@@ -62,7 +62,7 @@ function tripal_library_menu() {
     'title' => 'Libraries',
     'description' => 'Any biological library. Examples of genomic libraries include BAC, cDNA, FOSMID, etc.',
     'page callback' => 'tripal_library_admin_libraries_listing',
-    'access arguments' => array('administer tripal libraries'),
+    'access arguments' => array('administer tripal library'),
     'type' => MENU_NORMAL_ITEM,
   );
 
@@ -71,7 +71,7 @@ function tripal_library_menu() {
     'description' => 'Basic Description of Tripal Library Module Functionality',
     'page callback' => 'theme',
     'page arguments' => array('tripal_library_help'),
-    'access arguments' => array('administer tripal libraries'),
+    'access arguments' => array('administer tripal library'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
@@ -81,7 +81,7 @@ function tripal_library_menu() {
     'description' => 'Configure the Tripal Library module',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_library_admin'),
-    'access arguments' => array('administer tripal libraries'),
+    'access arguments' => array('administer tripal library'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
@@ -99,7 +99,7 @@ function tripal_library_menu() {
     'title' => 'Enable Library Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
     'page arguments' => array('tripal_library_admin_libraries', 'admin/tripal/chado/tripal_library'),
-    'access arguments' => array('administer tripal libraries'),
+    'access arguments' => array('administer tripal library'),
     'type' => MENU_CALLBACK,
   );
 

tripal_natural_diversity/tripal_natural_diversity.module

@@ -12,6 +12,20 @@ require_once('includes/tripal_natural_diversity.admin.inc');
  * @}
  */
 
+/**
+ *  Set the permission types that the chado module uses.  Essentially we
+ *  want permissionis
+ *
+ * @ingroup tripal_natural_diversity
+ */
+function tripal_natural_diversity_permission() {
+  return array(
+    'adminster tripal nd' => array(
+      'title' => t('Administer Natural Diversity Module'),
+      'description' => t('Allow users to administer the natural diversity module.'),
+    ),
+  );
+}
 /**
  *  Menu items are automatically added for the new node types created
  *  by this module to the 'Create Content' Navigation menu item.  This function
@@ -27,7 +41,7 @@ function tripal_natural_diversity_menu() {
    'title' => 'Natural Diversity Experiments',
    'description' => 'Experiments relating to natural diversity such as genotype and phenotype experiments.',
    'page callback' => 'tripal_natural_diversity_admin_natdiv_view',
-   'access arguments' => array('adminster tripal natural_diversity'),
+   'access arguments' => array('adminster tripal nd'),
    'type' => MENU_NORMAL_ITEM,
   );
 
@@ -36,7 +50,7 @@ function tripal_natural_diversity_menu() {
     'description' => ('Help for the Tripal natural diversity module.'),
     'page callback' => 'theme',
     'page arguments' => array('tripal_natural_diversity_help'),
-    'access arguments' => array('administer tripal natual_diversity'),
+    'access arguments' => array('administer tripal nd'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
@@ -45,7 +59,7 @@ function tripal_natural_diversity_menu() {
     'title' => 'Enable Natural Diversity Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
     'page arguments' => array('tripal_natural_diversity_admin_natdiv_exp', 'admin/tripal/chado/tripal_natdiv'),
-    'access arguments' => array('administer tripal natural_diversity'),
+    'access arguments' => array('administer tripal nd'),
     'type' => MENU_CALLBACK,
   );
 

tripal_organism/api/tripal_organism.api.inc

@@ -1,7 +1,7 @@
 <?php
 
 /**
- * @defgroup tripal_library_api Organism API
+ * @defgroup tripal_organism_api Organism API
  * @ingroup tripal_api
  * @{
  * Provides an application programming interface (API) to manage organisms

tripal_organism/includes/tripal_organism.chado_node.inc

@@ -260,13 +260,14 @@ function chado_organism_delete($node) {
   $check_feature = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
   $sql = "SELECT library_id FROM {library} WHERE organism_id = :organism_id";
   $check_lib = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
-
-  if (!$check_lib && !$check_feature) {
+  $sql = "SELECT stock_id FROM {stock} WHERE organism_id = :organism_id";
+  $check_stock = chado_query($sql, array(':organism_id' => $organism_id))->fetchObject();
+  
+  if (!$check_lib && !$check_feature && !$check_stock) {
     tripal_core_chado_delete('organism', array('organism_id' => $organism_id));
   }
   else {
-    drupal_set_message(t("Organism deleted from drupal. Warning: at least one " .
-        "library or feature depends on this organism. It was not removed from chado."));
+    drupal_set_message(t("Warning: other data depends on this organism. The organism page was removed from this site but the organism was removed from Chado."), 'warning');
   }
 }
 
@@ -412,8 +413,16 @@ function chado_organism_load($nodes) {
 function tripal_organism_node_presave($node) {
   switch ($node->type) {
     case 'chado_organism':
-      // set the title for the node
-      $node->title = "$node->genus $node->species";
+      // for a form submission the fields part of the node object
+      // but for a sync the feilds are in an object of the node
+      if(property_exists($node, 'organism')) {
+        // set the title
+        $node->title = $node->organism->genus . " " . $node->organism->species;
+      } 
+      else {
+        // set the title
+        $node->title = $node->genus  . " " . $node->species;
+      }
       break;
   }
 }

tripal_organism/theme/tripal_organism/tripal_organism_description.tpl.php

@@ -6,6 +6,6 @@ $organism = $variables['node']->organism;
    <table id="tripal_organism-table-description" class="tripal_organism-table tripal-table tripal-table-horz">
       <tr class="tripal_organism-table-odd-row tripal-table-even-row">
         <td><?php print $organism->comment; ?></td>
-      </tr>        	                                
+      </tr>                                          
    </table>
 </div>

tripal_phenotype/tripal_phenotype.module

@@ -8,6 +8,21 @@
  * @}
  */
 
+/**
+ *  Set the permission types that the chado module uses.  Essentially we
+ *  want permissionis
+ *
+ * @ingroup tripal_phenotype
+ */
+function tripal_phenotype_permission() {
+  return array(
+    'adminster tripal phenotype' => array(
+      'title' => t('Administer Phenotype Module'),
+      'description' => t('Allow users to administer the phenotype module.'),
+    ),
+  );
+}
+
 /**
  *  Menu items are automatically added for the new node types created
  *  by this module to the 'Create Content' Navigation menu item.  This function

tripal_project/includes/tripal_project.chado_node.inc

@@ -408,30 +408,30 @@ function chado_project_node_access($node, $op, $account) {
  */
 function tripal_project_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
-  	case 'chado_project':
-  	  // Show feature browser and counts
-  	  if ($view_mode == 'full') {
-  	    $node->content['tripal_project_base'] = array(
-  	      '#value' => theme('tripal_project_base', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_project_contact'] = array(
-  	      '#value' => theme('tripal_project_contact', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_project_properties'] = array(
-  	      '#value' => theme('tripal_project_properties', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_project_publications'] = array(
-  	      '#value' => theme('tripal_project_publications', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_project_relationships'] = array(
-  	      '#value' => theme('tripal_project_relationships', array('node' => $node)),
-  	    );
-  	  }
-  	  if ($view_mode == 'teaser') {
-  	    $node->content['tripal_project_teaser'] = array(
-  	      '#value' => theme('tripal_project_teaser', array('node' => $node)),
-  	    );
-  	  }
-  	  break;
+    case 'chado_project':
+      // Show feature browser and counts
+      if ($view_mode == 'full') {
+        $node->content['tripal_project_base'] = array(
+          '#value' => theme('tripal_project_base', array('node' => $node)),
+        );
+        $node->content['tripal_project_contact'] = array(
+          '#value' => theme('tripal_project_contact', array('node' => $node)),
+        );
+        $node->content['tripal_project_properties'] = array(
+          '#value' => theme('tripal_project_properties', array('node' => $node)),
+        );
+        $node->content['tripal_project_publications'] = array(
+          '#value' => theme('tripal_project_publications', array('node' => $node)),
+        );
+        $node->content['tripal_project_relationships'] = array(
+          '#value' => theme('tripal_project_relationships', array('node' => $node)),
+        );
+      }
+      if ($view_mode == 'teaser') {
+        $node->content['tripal_project_teaser'] = array(
+          '#value' => theme('tripal_project_teaser', array('node' => $node)),
+        );
+      }
+      break;
   }
 }

tripal_project/tripal_project.module

@@ -38,7 +38,7 @@ function tripal_project_menu() {
     'title' => 'Projects',
     'description' => ('A project. Can be used for grouping data such as with the natural diversity module data.'),
     'page callback' => 'tripal_project_admin_project_view',
-    'access arguments' => array('adminster tripal projects'),
+    'access arguments' => array('adminster tripal project'),
     'type' => MENU_NORMAL_ITEM
   );
 
@@ -47,7 +47,7 @@ function tripal_project_menu() {
     'description' => ("Basic Description of Tripal Project Module Functionality."),
     'page callback' => 'theme',
     'page arguments' => array('tripal_project_help'),
-    'access arguments' => array('adminster tripal projects'),
+    'access arguments' => array('adminster tripal project'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 6
   );
@@ -56,7 +56,7 @@ function tripal_project_menu() {
     'title' => 'Settings',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_project_admin'),
-    'access arguments' => array('adminster tripal projects'),
+    'access arguments' => array('adminster tripal project'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 4
   );
@@ -66,7 +66,7 @@ function tripal_project_menu() {
     'description' => 'Create pages on this site for projects stored in Chado',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_core_chado_node_sync_form', 'tripal_project', 'chado_project'),
-    'access arguments' => array('administer tripal projects'),
+    'access arguments' => array('administer tripal project'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
@@ -75,7 +75,7 @@ function tripal_project_menu() {
     'title' => 'Enable Project Administrative View',
     'page callback' => 'tripal_views_admin_enable_view',
     'page arguments' => array('tripal_project_admin_projects', 'admin/tripal/chado/tripal_project'),
-    'access arguments' => array('administer tripal projects'),
+    'access arguments' => array('administer tripal project'),
     'type' => MENU_CALLBACK,
   );
 

tripal_pub/includes/tripal_pub.chado_node.inc

@@ -940,46 +940,46 @@ function chado_pub_delete(&$node) {
  */
 function tripal_pub_node_view($node, $view_mode, $langcode) {
   switch ($node->type) {
-  	case 'chado_pub':
-  	  // Show feature browser and counts
-  	  if ($view_mode == 'full') {
-  	    $node->content['tripal_pub_authors'] = array(
-  	      '#value' => theme('tripal_pub_authors', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_base'] = array(
-  	      '#value' => theme('tripal_pub_base', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_featuremaps'] = array(
-  	      '#value' => theme('tripal_pub_featuremaps', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_features'] = array(
-  	      '#value' => theme('tripal_pub_features', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_libraries'] = array(
-  	      '#value' => theme('tripal_pub_libraries', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_projects'] = array(
-  	      '#value' => theme('tripal_pub_projects', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_properties'] = array(
-  	      '#value' => theme('tripal_pub_properties', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_references'] = array(
-  	      '#value' => theme('tripal_pub_references', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_relationships'] = array(
-  	      '#value' => theme('tripal_pub_relationships', array('node' => $node)),
-  	    );
-  	    $node->content['tripal_pub_stocks'] = array(
-  	      '#value' => theme('tripal_pub_stocks', array('node' => $node)),
-  	    );
-  	  }
-  	  if ($view_mode == 'teaser') {
-  	    $node->content['tripal_pub_teaser'] = array(
-  	      '#value' => theme('tripal_pub_teaser', array('node' => $node)),
-  	    );
-  	  }
-  	  break;
+    case 'chado_pub':
+      // Show feature browser and counts
+      if ($view_mode == 'full') {
+        $node->content['tripal_pub_authors'] = array(
+          '#value' => theme('tripal_pub_authors', array('node' => $node)),
+        );
+        $node->content['tripal_pub_base'] = array(
+          '#value' => theme('tripal_pub_base', array('node' => $node)),
+        );
+        $node->content['tripal_pub_featuremaps'] = array(
+          '#value' => theme('tripal_pub_featuremaps', array('node' => $node)),
+        );
+        $node->content['tripal_pub_features'] = array(
+          '#value' => theme('tripal_pub_features', array('node' => $node)),
+        );
+        $node->content['tripal_pub_libraries'] = array(
+          '#value' => theme('tripal_pub_libraries', array('node' => $node)),
+        );
+        $node->content['tripal_pub_projects'] = array(
+          '#value' => theme('tripal_pub_projects', array('node' => $node)),
+        );
+        $node->content['tripal_pub_properties'] = array(
+          '#value' => theme('tripal_pub_properties', array('node' => $node)),
+        );
+        $node->content['tripal_pub_references'] = array(
+          '#value' => theme('tripal_pub_references', array('node' => $node)),
+        );
+        $node->content['tripal_pub_relationships'] = array(
+          '#value' => theme('tripal_pub_relationships', array('node' => $node)),
+        );
+        $node->content['tripal_pub_stocks'] = array(
+          '#value' => theme('tripal_pub_stocks', array('node' => $node)),
+        );
+      }
+      if ($view_mode == 'teaser') {
+        $node->content['tripal_pub_teaser'] = array(
+          '#value' => theme('tripal_pub_teaser', array('node' => $node)),
+        );
+      }
+      break;
   }
 }
 /**

tripal_pub/includes/tripal_pub.pub_search.inc

@@ -159,16 +159,13 @@ function tripal_pub_search_form($form, &$form_state) {
     '#default_value' => $num_criteria,
   );
   
-  if (user_access('access administration pages')) {
-    $form['admin-instructions'] = array(
-      '#prefix' => '<div class="tripal-no-results">',
-      '#markup'  =>  t('Administrators, you can select the fields with which a user can use to search,
-          by checking the desired fields on the ' .
-          l('Publication Module Settings Page', 'admin/tripal/chado/tripal_pub/configuration'). ' in
-         the section titled "Search Options".  The selected fields will appear in the dropdowns below.'),
-      '#suffix' => '</div>'
-    );
-  }
+  $form['admin-instructions'] = array(
+    '#markup'  =>  theme('tripal_admin_message', array('message' => 
+      t('Administrators, you can select the fields with which a user can use to search,
+         by checking the desired fields on the ' .
+         l('Publication Module Settings Page', 'admin/tripal/chado/tripal_pub/configuration'). ' in
+        the section titled "Search Options".  The selected fields will appear in the dropdowns below.'))),
+  ); 
   $form['instructions'] = array(
     '#markup'  =>  t('To search for publications enter keywords in the text boxes below.  
         You can limit your search by selecting the field in the dropdown box. Click the 

tripal_pub/theme/tripal_pub_help.tpl.php

@@ -6,106 +6,106 @@ module additionally provides a search tool for finding publications that
 have been added to Chado database.</p>
 <h3>Setup Instructions:</h3>
 <ol>
-	<li>
-	<p><b>Set Permissions</b>: The publication module supports the Drupal
-	user permissions interface for controlling access to publication
-	content and functions. These permissions include viewing, creating,
-	editing or administering of publications. The default is that only the
-	original site administrator has these permissions. You can <a
-		href="<?php print url('admin/user/roles') ?>">add roles</a> for
-	classifying users, <a href="<?php print url('admin/user/user') ?>">assign
-	users to roles</a> and <a
-		href="<?php print url('admin/user/permissions') ?>">assign permissions</a>
-	for the publication content to those roles. For a simple setup, allow
-	anonymous users access to view publication content and allow the site
-	administrator all other permissions.</p>
-	</li>
-	<li>
-	<p><b>Sync Publications</b>: If you already have publications in your
-	Chado database, or you loaded them through a means other than Tripal,
-	and you want those publications to appear on your site then you will
-	need to "sync" them with Drupal. Use the <?php print l('sync publications', 'admin/tripal/tripal_pub/sync') ?>
-	page to sync all publications.</p>
-	</li>
-	<li>
-	<p><b>Configure the Search Behavior</b>: Before allowing site visitors
-	to search for publications visit the <?php print l('configuration page', 'admin/tripal/tripal_pub/configuration') ?>
-	to disable or enable fields for searching. Tripal uses its own ontology
-	for storing publication information in Chado, and all child terms of
-	the "Publication Details" are made available for searching. However,
-	some of these may not be desired for searching and can be disabled.</p>
-	</li>
-	<li>
-	<p><b>AGL Importer</b>: Initially, the Tripal publication module
-	supports creating publication importers using PubMed and the USDA
-	National Agricultural Library (AGL). The AGL database uses a Z39.50
-	protocol for querying and therefore Tripal requires the 'YAZ' library
-	to connect. Before you can query AGL you must install the YAZ library
-	and the PHP YAZ library. The following steps can be used on an Ubuntu
-	12.04 server to intall the necessary pre-requisites:</p>
-	<ol>
-		<li>Install the YAZ libraries: sudo apt-get install yaz libyaz4-dev</li>
-		<li>Install the PHP YAZ extension: sudo pecl install yaz</li>
-		<li>Add the text 'extension=yaz.so' to the appropriate php.ini file
-		(e.g. /etc/php5/apache2filter/php.ini). On Ubuntu you may need to
-		add it to the php.ini file specfic for the Apache webserver and 
-		also to the php.ini specific for the command-line.</li>
-		<li>Restart the webserver</li>
-	</ol>
-	</li>
-	<li>
-	<p><b>Automate Importers:</b> Site administrators can <?php print l('create publication importers', 'admin/tripal/tripal_pub/import/new') ?>
-	that can be used to query remote databases (e.g. PubMed) and import
-	publications into this database. After creation of importers you can
-	automate import of publications into the site by creating a cron job
-	with a <?php print l('Drush', "http://drupal.org/project/drush")?>
-	command. The cron job can be setup to run the importers periodically.
-	The following is an example entry, added to the 'root' crontab, that
-	would run importers on a weekly bases (Friday at 9am): <br>
-	</p>
-	<pre>0 9 * * 5  su - [web user] -c 'cd [drupal install path]; drush -l http://[site url] tpubs-import --report=[email]'</pre>
-	Where:<br>
-	<p>[web user] is the name of the user on the system under which the web
-	server runs<br>
-	[drupal install path] is the location where drupal is installed<br>
-	[site url] is the URL path for the site <br>
-	[email] is the email address of the person who should receive an HTML
-	report of the publications added. Separate multiple emails with a comma
-	(no spaces).<br>
-	The --report=Y option indicates that an HTML style report should be
-	generated listing the publications that were added. If this options is
-	not used then no report is generated.</p>
-	</li>
+  <li>
+  <p><b>Set Permissions</b>: The publication module supports the Drupal
+  user permissions interface for controlling access to publication
+  content and functions. These permissions include viewing, creating,
+  editing or administering of publications. The default is that only the
+  original site administrator has these permissions. You can <a
+    href="<?php print url('admin/user/roles') ?>">add roles</a> for
+  classifying users, <a href="<?php print url('admin/user/user') ?>">assign
+  users to roles</a> and <a
+    href="<?php print url('admin/user/permissions') ?>">assign permissions</a>
+  for the publication content to those roles. For a simple setup, allow
+  anonymous users access to view publication content and allow the site
+  administrator all other permissions.</p>
+  </li>
+  <li>
+  <p><b>Sync Publications</b>: If you already have publications in your
+  Chado database, or you loaded them through a means other than Tripal,
+  and you want those publications to appear on your site then you will
+  need to "sync" them with Drupal. Use the <?php print l('sync publications', 'admin/tripal/tripal_pub/sync') ?>
+  page to sync all publications.</p>
+  </li>
+  <li>
+  <p><b>Configure the Search Behavior</b>: Before allowing site visitors
+  to search for publications visit the <?php print l('configuration page', 'admin/tripal/tripal_pub/configuration') ?>
+  to disable or enable fields for searching. Tripal uses its own ontology
+  for storing publication information in Chado, and all child terms of
+  the "Publication Details" are made available for searching. However,
+  some of these may not be desired for searching and can be disabled.</p>
+  </li>
+  <li>
+  <p><b>AGL Importer</b>: Initially, the Tripal publication module
+  supports creating publication importers using PubMed and the USDA
+  National Agricultural Library (AGL). The AGL database uses a Z39.50
+  protocol for querying and therefore Tripal requires the 'YAZ' library
+  to connect. Before you can query AGL you must install the YAZ library
+  and the PHP YAZ library. The following steps can be used on an Ubuntu
+  12.04 server to intall the necessary pre-requisites:</p>
+  <ol>
+    <li>Install the YAZ libraries: sudo apt-get install yaz libyaz4-dev</li>
+    <li>Install the PHP YAZ extension: sudo pecl install yaz</li>
+    <li>Add the text 'extension=yaz.so' to the appropriate php.ini file
+    (e.g. /etc/php5/apache2filter/php.ini). On Ubuntu you may need to
+    add it to the php.ini file specfic for the Apache webserver and 
+    also to the php.ini specific for the command-line.</li>
+    <li>Restart the webserver</li>
+  </ol>
+  </li>
+  <li>
+  <p><b>Automate Importers:</b> Site administrators can <?php print l('create publication importers', 'admin/tripal/tripal_pub/import/new') ?>
+  that can be used to query remote databases (e.g. PubMed) and import
+  publications into this database. After creation of importers you can
+  automate import of publications into the site by creating a cron job
+  with a <?php print l('Drush', "http://drupal.org/project/drush")?>
+  command. The cron job can be setup to run the importers periodically.
+  The following is an example entry, added to the 'root' crontab, that
+  would run importers on a weekly bases (Friday at 9am): <br>
+  </p>
+  <pre>0 9 * * 5  su - [web user] -c 'cd [drupal install path]; drush -l http://[site url] tpubs-import --report=[email]'</pre>
+  Where:<br>
+  <p>[web user] is the name of the user on the system under which the web
+  server runs<br>
+  [drupal install path] is the location where drupal is installed<br>
+  [site url] is the URL path for the site <br>
+  [email] is the email address of the person who should receive an HTML
+  report of the publications added. Separate multiple emails with a comma
+  (no spaces).<br>
+  The --report=Y option indicates that an HTML style report should be
+  generated listing the publications that were added. If this options is
+  not used then no report is generated.</p>
+  </li>
 </ol>
 <h3>Features of this Module:</h3>
 <ul>
 
-	<li>
-	<p><b>Add/Edit/Delete Publications</b>: Publications can be maually
-	added <?php  l('here', 'node/add/chado-pub') ?>. Once added,
-	publications can be modified or deleted by clicking the Edit tab at the
-	top of a publication page.</p>
-	</li>
+  <li>
+  <p><b>Add/Edit/Delete Publications</b>: Publications can be maually
+  added <?php  l('here', 'node/add/chado-pub') ?>. Once added,
+  publications can be modified or deleted by clicking the Edit tab at the
+  top of a publication page.</p>
+  </li>
 
-	<li>
-	<p><b>Publication Search Tool</b>: A <?php print l('search tool','find/publications') ?>
-	is provided for finding publications. Unlike most default search tools
-	for Tripal, this tool does not rely on Drupal Views</p>
-	</li>
+  <li>
+  <p><b>Publication Search Tool</b>: A <?php print l('search tool','find/publications') ?>
+  is provided for finding publications. Unlike most default search tools
+  for Tripal, this tool does not rely on Drupal Views</p>
+  </li>
 
-	<li>
-	<p><b>Bulk Import of Publications</b>: Site administrators can <?php print l('add a new publication importer', 'admin/tripal/tripal_pub/import/new') ?>
-	which provides a set of search terms for querying a remote publication
-	database (e.g. PubMed). Publications that matche the search terms can
-	be imported when the publication import cron command is executed. The
-	cron command can be executed using the Drush command: drush
-	tpubs-import. This drush command can be added as a system-wide cron (in
-	the same way the Tripal jobs cron is implemented) to be executed on a
-	periodic basis. This will allow the site to import publications which
-	have been newly added to remote databases and which are relative to the
-	site. Site administrators can <?php print l('see the list of importers', 'admin/tripal/tripal_pub/import_list') ?>
-	and edit, disable or delete the importers.</p>
-	</li>
+  <li>
+  <p><b>Bulk Import of Publications</b>: Site administrators can <?php print l('add a new publication importer', 'admin/tripal/tripal_pub/import/new') ?>
+  which provides a set of search terms for querying a remote publication
+  database (e.g. PubMed). Publications that matche the search terms can
+  be imported when the publication import cron command is executed. The
+  cron command can be executed using the Drush command: drush
+  tpubs-import. This drush command can be added as a system-wide cron (in
+  the same way the Tripal jobs cron is implemented) to be executed on a
+  periodic basis. This will allow the site to import publications which
+  have been newly added to remote databases and which are relative to the
+  site. Site administrators can <?php print l('see the list of importers', 'admin/tripal/tripal_pub/import_list') ?>
+  and edit, disable or delete the importers.</p>
+  </li>
 
 
 

tripal_pub/tripal_pub.module

@@ -64,7 +64,7 @@ function tripal_pub_menu() {
     'title' => 'Publications',
     'description' => ('A documented provenance artefact - publications, documents, personal communication.'),
     'page callback' => 'tripal_pub_admin_pub_view',
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type' => MENU_NORMAL_ITEM
   );
 
@@ -73,7 +73,7 @@ function tripal_pub_menu() {
     'description' => ('A module for interfacing the GMOD chado database with Drupal, providing viewing of publications'),
     'page callback' => 'theme',
     'page arguments' => array('tripal_pub_help'),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
@@ -83,7 +83,7 @@ function tripal_pub_menu() {
     'description' => 'Configure the Tripal publication module.',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_pub_admin'),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
@@ -104,7 +104,7 @@ function tripal_pub_menu() {
     'description' => 'Update publication citations',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_pub_citation_form'),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 1
   );
@@ -113,7 +113,7 @@ function tripal_pub_menu() {
     'title' => t('Importers'),
     'description' => t('List all publication importers'),
     'page callback' => 'tripal_pub_importers_list',
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
@@ -131,65 +131,48 @@ function tripal_pub_menu() {
     'title' => t('Add an Importer'),
     'description' => t('Add a new publication importer.'),
     'page callback' => 'tripal_pub_importer_setup_page',
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type ' => MENU_CALLBACK,
   );
 
   $items['admin/tripal/chado/tripal_pub/import/raw/%'] = array(
     'page callback' => 'tripal_pub_get_raw_data',
     'page arguments' => array(6),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type ' => MENU_CALLBACK,
   );
 
   $items['admin/tripal/chado/tripal_pub/import/edit/%'] = array(
     'page callback' => 'tripal_pub_importer_setup_page',
     'page arguments' => array(5, 6),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type ' => MENU_CALLBACK,
   );
 
   $items['admin/tripal/chado/tripal_pub/import/submit/%'] = array(
     'page callback' => 'tripal_pub_importer_submit_job',
     'page arguments' => array(6),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type ' => MENU_CALLBACK,
   );
 
   $items['admin/tripal/chado/tripal_pub/import/delete/%'] = array(
     'page callback' => 'tripal_pub_importer_delete',
     'page arguments' => array(5),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type ' => MENU_CALLBACK,
   );
   $items['admin/tripal/chado/tripal_pub/import/changedb'] = array(
     'page callback' => 'tripal_pub_importer_setup_page_update_remotedb',
     'page arguments' => array(),
-    'access arguments' => array('administer tripal pubs'),
+    'access arguments' => array('administer tripal pub'),
     'type ' => MENU_CALLBACK,
   );
 
   $items['admin/tripal/chado/tripal_pub/import/criteria/%/%'] = array(
     'page callback' => 'tripal_pub_importer_setup_page_update_criteria',
     'page arguments' => array(5, 6),
-    'access arguments' => array('administer tripal pubs'),
-    'type ' => MENU_CALLBACK,
-  );
-
-  $items['tripal_pub/chado/properties/add'] = array(
-    'page callback' => 'tripal_pub_property_add',
-    'access arguments' => array('edit chado_pub content'),
-    'type ' => MENU_CALLBACK,
-  );
-  $items['tripal_pub/chado/properties/description'] = array(
-    'page callback' => 'tripal_pub_property_get_description',
-    'access arguments' => array('edit chado_pub content'),
-    'type ' => MENU_CALLBACK,
-  );
-  $items['tripal_pub/chado/properties/minus/%/%'] = array(
-    'page callback' => 'tripal_pub_property_delete',
-    'page arguments' => array(3, 4),
-    'access arguments' => array('edit chado_pub content'),
+    'access arguments' => array('administer tripal pub'),
     'type ' => MENU_CALLBACK,
   );
 

tripal_stock/includes/tripal_stock.chado_node.inc

@@ -783,7 +783,16 @@ function tripal_stock_node_presave($node) {
 
   switch ($node->type) {
     case 'chado_stock':
-      $values = array('organism_id' => $node->organism_id);
+      // for a form submission the fields part of the node object
+      // but for a sync the feilds are in an object of the node
+      $organism_id = null;
+      if(property_exists($node, 'stock')) {
+        $organism_id = $node->stock->organism_id;
+      }
+      else {
+        $organism_id = $node->organism_id;
+      }
+      $values = array('organism_id' => $organism_id);
       $organism = tripal_core_chado_select('organism', array('genus','species'), $values);
       $values = array('cvterm_id' => $node->type_id);
       $cvterm = tripal_core_chado_select('cvterm', array('name'), $values);
@@ -873,7 +882,7 @@ function tripal_stock_node_view($node, $view_mode, $langcode) {
     case 'chado_organism':
       if ($view_mode == 'full') {
         $node->content['tripal_organism_stocks'] = array(
-          '#value' => theme('tripal_organism_stocks', $node),
+          '#value' => theme('tripal_organism_stocks', array('node' => $node)),
         );
       }
       break;

tripal_stock/theme/tripal_organism/tripal_organism_stocks.tpl.php

@@ -44,7 +44,7 @@ if (count($stocks) > 0) { ?>
           <td><?php
             $name = $stock->name;
             if (!$stock->name) {
-            	$name = $stock->uniquename;
+              $name = $stock->uniquename;
             }
             if ($stock->nid) {    
               print l($name, "node/$stock->nid", array('attributes' => array('target' => '_blank')));        

tripal_stock/tripal_stock.module

@@ -39,12 +39,20 @@ require_once("api/tripal_stock.api.inc");
 function tripal_stock_menu() {
   $items = array();
 
+  // the menu link for addressing any stock (by name, uniquename, synonym)
+  $items['stock/%'] = array(
+    'page callback' => 'tripal_stock_match_stocks_page',
+    'page arguments' => array(1),
+    'access arguments' => array('access chado_stock content'),
+    'type' => MENU_LOCAL_TASK,
+  );
+  
   //Administrative settings menu-----------------
   $items['admin/tripal/chado/tripal_stock'] = array(
     'title' => 'Stocks',
     'description' => 'A stock is the physical entities of an organism, either living or preserved.',
     'page callback' => 'tripal_stock_admin_stock_view',
-    'access arguments' => array('administer tripal stocks'),
+    'access arguments' => array('administer tripal stock'),
     'type' => MENU_NORMAL_ITEM
   );
 
@@ -53,7 +61,7 @@ function tripal_stock_menu() {
     'description' => 'Settings for Chado Stocks',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_stock_admin'),
-    'access arguments' => array('administer tripal stocks'),
+    'access arguments' => array('administer tripal stock'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 5
   );
@@ -64,7 +72,7 @@ function tripal_stock_menu() {
     'page callback' => 'drupal_get_form',
     //'page arguments' => array('tripal_stock_sync_form'),
     'page arguments' => array('tripal_core_chado_node_sync_form', 'tripal_stock', 'chado_stock'),
-    'access arguments' => array('administer tripal stocks'),
+    'access arguments' => array('administer tripal stock'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 0
   );
@@ -74,18 +82,12 @@ function tripal_stock_menu() {
     'description' => 'Basic Description of Tripal Stock Module Functionality',
     'page callback' => 'theme',
     'page arguments' => array('tripal_stock_help'),
-    'access arguments' => array('administer tripal stocks'),
+    'access arguments' => array('administer tripal stock'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10
   );
 
-  // the menu link for addressing any stock (by name, uniquename, synonym)
-  $items['stock/%'] = array(
-    'page callback' => 'tripal_stock_match_stocks_page',
-    'page arguments' => array(1),
-    'access arguments' => array('access chado_stock content'),
-    'type' => MENU_LOCAL_TASK,
-  );
+
   return $items;
 }
 

tripal_views/tripal_views.views.inc

@@ -569,35 +569,35 @@ function tripal_views_views_data_alter(&$data) {
           //      without 1st needing to add relationship to organism table
           $base_field = $base_table . '_id';
           $data[$linker_table][$base_field] = array(
-			      'group' => $base_title,
-			      'title' => $base_title . 'Node',
-			      'help' => "Links $base_title to it's node.",
-			      'relationship' => array(
-			        'handler' => 'views_handler_relationship',
-			        'title' => t("$base_title => Node"),
-			        'label' => t("$base_title => Node"),
-			        'real field' => 'nid',
-			        'base' => 'node',
-			        'base field' => 'nid'
-			      ),
-			    );
+            'group' => $base_title,
+            'title' => $base_title . 'Node',
+            'help' => "Links $base_title to it's node.",
+            'relationship' => array(
+              'handler' => 'views_handler_relationship',
+              'title' => t("$base_title => Node"),
+              'label' => t("$base_title => Node"),
+              'real field' => 'nid',
+              'base' => 'node',
+              'base field' => 'nid'
+            ),
+          );
 
           // Add Chado fields to a node-based view
           // This will only be done with relationships
           $base_field = $base_table . '_id';
           $data['node'][$base_field] = array(
-			      'group' => $base_title,
-			      'title' => $base_title,
-			      'help' => "Links node to chado $base_title.",
-			      'relationship' => array(
-			        'handler' => 'views_handler_relationship',
-			        'title' => t("Node => $base_title"),
-			        'label' => t("Node => $base_title"),
-			        'real field' => 'nid',
-			        'base' => $linker_table,
-			        'base field' => 'nid'
-			      ),
-			    );
+            'group' => $base_title,
+            'title' => $base_title,
+            'help' => "Links node to chado $base_title.",
+            'relationship' => array(
+              'handler' => 'views_handler_relationship',
+              'title' => t("Node => $base_title"),
+              'label' => t("Node => $base_title"),
+              'real field' => 'nid',
+              'base' => $linker_table,
+              'base field' => 'nid'
+            ),
+          );
 
         }
       }