Updated node template CSS... working on adding node template details on each content block

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_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

@@ -1,152 +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;
-  text-align: left;
-  vertical-align: top;
-  padding: 0px 0px 0px 20px;
+.tripal-contents-table-tr {
+  padding: 0px !important;
+  margin:  0px !important;
+  border:  none !important;
+  background-color: transparent !important;
 }
-.tripal_contents_table_td_toc { 
+.tripal-contents-table-td-toc { 
   border: 1px solid #888888 !important;
+  margin:  0px !important;
   padding: 10px !important;
-  background: none repeat scroll 0 0 rgba(0, 0, 0, 0.063);
-}
-.tripal_contents_table_tr {
-background-color: transparent;
+  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 10px;
-  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 {
-  min-height: 400px;
-  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;
@@ -160,9 +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
@@ -79,7 +70,7 @@ else { ?>
 })(jQuery);
 </script>
 
-<div id="tripal_<?php print $ttype?>_content" class="tripal_contents"> <?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">
@@ -87,48 +78,43 @@ else { ?>
       </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">
-        <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
-               }
+  <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

@@ -453,9 +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
@@ -526,5 +534,37 @@ function tripal_core_views_api() {
   );
 }
 
-
-
+/**
+ * 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_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_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
+    }
   }
 }
 /**

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_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_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_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;