Added backwards compatibility support for field_resource_* CCK fields

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

@@ -21,7 +21,7 @@ else {
         var id = $(this).attr('id') + "-tripal-data-block";
         $(".tripal-data-block").hide().filter("#"+ id).fadeIn('fast');
         return false;
-      }); 
+      });
   
       // if a ?block= is specified in the URL then we want to show the
       // requested block

tripal_core/tripal_core.module

@@ -557,114 +557,172 @@ function tripal_core_node_view_alter(&$build) {
       // examine elements without a '#' prefix as these should be adding
       // contents to the page. Skip the table of contents and links as those
       // will be placed elsewhere
-      if (!preg_match('/^#/', $key) and $key != 'tripal_toc' and $key != 'links') {
-
-        //-----------------------
-        // INITIALIZE THE CONTENT VARIABLES
-        //-----------------------
-        $toc_item_title = $key;
-        $toc_item_id    = $key;
-        $toc_item_link  = '';
-
-        // get the title for the table of contents.  Tripal templates should
-        // have a '#tripal_toc_title' element in the build array
-        if (array_key_exists('#tripal_toc_title', $build[$key])) {
-          $toc_item_title = $build[$key]['#tripal_toc_title'];
+      if (preg_match('/^#/', $key) or $key == 'tripal_toc' or $key == 'links') {
+        continue;
+      }
+      
+      // for backwards compatibility we will handle the content type fields 
+      // named 'field_resource_blocks', 'field_resource_titles', and 'field_resource_links'
+      // these fields can be added on the Drupal content types page and were
+      // specifically recoginzed by Tripal v1.1. 
+      if ($key == "field_resource_links") {
+        // links should just appear on the sidebar as is and not open up a panel
+        foreach (element_children($build[$key]) as $index) {
+          $element = $build[$key][$index];
+          $weight = 0;
+          $parts = explode("|", $element['#markup']);
+          $toc[$weight][$parts[0]] = l($parts[0], $parts[1], array('attributes' => array('class' => 'tripal-field-resource_link')));
+          // remove this link from the build array as we've moved it to appear in the TOC
+          unset($build[$key]);
         }
-        // other elements in the $build array may just have a '#title' element,
-        if (array_key_exists('#title', $build[$key])) {
-          $toc_item_title = $build[$key]['#title'];
+        continue;
+      }
+      if ($key == "field_resource_titles") {
+        // ignore these, we will use them in the field_resource_blocks if
+        // statement below
+        continue;
+      }
+      if ($key == "field_resource_blocks") {
+        foreach (element_children($build[$key]) as $index) {
+          // get the block details and the title
+          $weight = 0;
+          $markup = $build[$key][$index]["#markup"];
+          $toc_item_id = "resource-$index";
+          $toc_item_title = $build["field_resource_titles"][$index]["#markup"];
+          $updated_markup = "
+            <div id=\"$toc_item_id-tripal-data-block\" class=\"tripal-data-block\">
+              <div class=\"$toc_item_id-tripal-data-block-title tripal-data-block-title\">$toc_item_title</div>
+                $markup
+              </div>
+            </div>
+          ";
+          $build[$toc_item_id]['#markup'] = $updated_markup;
+          $build[$toc_item_id]['#weight'] = $weight;
+          $build[$toc_item_id]['#toc_handled'] = TRUE;
+          // add the entry to the TOC
+          $toc_item_link = "<div class=\"tripal_toc_list_item\"><a id=\"$toc_item_id\" class=\"tripal_toc_list_item_link\" href=\"?block=$toc_item_id\">$toc_item_title</a></div>";
+          $toc[$weight][$toc_item_title] = $toc_item_link;
         }
-        $toc_item_title = ucwords($toc_item_title);
+        // remove the key from the build array. We have have replaced it
+        unset($build[$key]);
+        unset($build["field_resource_titles"]);
+        continue;
+      }
+      
+      // skip any keys we may have already handled. This is the case for 
+      // the field_resource_blocks where we removed the old CCK fields
+      // and added new ones.  We don't want these new ones to be processed
+      // again by the code below.
+      if (array_key_exists('#toc_handled', $build[$key]) and $build[$key]['#toc_handled'] == TRUE) {
+        continue;
+      }
+      
+      // for all other fields we will handle in the following way 
+      //-----------------------
+      // INITIALIZE THE CONTENT VARIABLES
+      //-----------------------
+      $toc_item_title = $key;
+      $toc_item_id    = $key;
+      $toc_item_link  = '';
+
+      // get the title for the table of contents.  Tripal templates should
+      // have a '#tripal_toc_title' element in the build array
+      if (array_key_exists('#tripal_toc_title', $build[$key])) {
+        $toc_item_title = $build[$key]['#tripal_toc_title'];
+      }
+      // other elements in the $build array may just have a '#title' element,
+      if (array_key_exists('#title', $build[$key])) {
+        $toc_item_title = $build[$key]['#title'];
+      }
+      $toc_item_title = ucwords($toc_item_title);
 
-        if (array_key_exists('#tripal_toc_id', $build[$key])) {
-          $toc_item_id = $build[$key]['#tripal_toc_id'];
-        }
-        $toc_item_link = "<div class=\"tripal_toc_list_item\"><a id=\"$toc_item_id\" class=\"tripal_toc_list_item_link\" href=\"?block=$toc_item_id\">$toc_item_title</a></div>";
+      if (array_key_exists('#tripal_toc_id', $build[$key])) {
+        $toc_item_id = $build[$key]['#tripal_toc_id'];
+      }
+      $toc_item_link = "<div class=\"tripal_toc_list_item\"><a id=\"$toc_item_id\" class=\"tripal_toc_list_item_link\" href=\"?block=$toc_item_id\">$toc_item_title</a></div>";
 
 
-        //-----------------------
-        // GET THE MARKUP FOR EACH ELEMENT
-        //-----------------------
-        $markup = '';
+      //-----------------------
+      // GET THE MARKUP FOR EACH ELEMENT
+      //-----------------------
+      $markup = '';
 
-        // find the markup. Some fields will have a '#markup' and others, such
-        // as CCK elements may have a set of '#markup' elements organized by
-        // numerical keys.
-        if (array_key_exists('#markup', $build[$key]) and trim($build[$key]['#markup'])) {
-          $markup = $build[$key]['#markup'];
-        }
-        // For backwards copmatibility we should support the '#value' element as well.
-        elseif (array_key_exists('#value', $build[$key]) and trim($build[$key]['#value'])) {
-          $markup = $build[$key]['#markup'];
-        }
+      // find the markup. Some fields will have a '#markup' and others, such
+      // as CCK elements may have a set of '#markup' elements organized by
+      // numerical keys.
+      if (array_key_exists('#markup', $build[$key]) and trim($build[$key]['#markup'])) {
+        $markup = $build[$key]['#markup'];
+      }
+      // For backwards copmatibility we should support the '#value' element as well.
+      elseif (array_key_exists('#value', $build[$key]) and trim($build[$key]['#value'])) {
+        $markup = $build[$key]['#markup'];
+      }
 
-        // if we have no '#markup' field then this element has not yet
-        // been rendered.  Let's render it and substitute that for markup
-        if (!$markup) {
-          $markup = trim(render($build[$key]));
-          $build[$key] = array(
-            '#markup' => $markup,
-          );
-        }
+      // if we have no '#markup' field then this element has not yet
+      // been rendered.  Let's render it and substitute that for markup
+      if (!$markup) {
+        $markup = trim(render($build[$key]));
+        $build[$key] = array(
+          '#markup' => $markup,
+        );
+      }
 
-        // if we still don't have markup then skip this one
-        if (!$markup) {
-          continue;
-        }
+      // if we still don't have markup then skip this one
+      if (!$markup) {
+        continue;
+      }
 
-        //-----------------------
-        // FIND THE TEMPLATE PATH
-        //-----------------------
-        // get the template path so we can put it in an admin message box
-        $path = '';
-        if (!array_key_exists('#tripal_template_show', $build[$key]) or 
-             $build[$key]['#tripal_template_show'] == TRUE) {
-          if ($cache and array_key_exists($key, $cache->data) and array_key_exists('path', $cache->data[$key])) {
-  
-            $path = $cache->data[$key]['path'] . '/' . $key . '.tpl.php';
-  
-            $path = tripal_set_message("Administrators, you can
-              customize the way the content above is presented.  Tripal provides a template
-              file for each block of content.  To customize, copy the template file to your
-              site's default theme, edit then " .
-              l('clear the Drupal cache', 'admin/config/development/performance', array('attributes' => array('target' => '_blank'))) . ".
-              Currently, the content above is provided by this template: <br><br>$path",
-              TRIPAL_INFO,
-              array('return_html' => 1)
-            );
-          }
+      //-----------------------
+      // FIND THE TEMPLATE PATH
+      //-----------------------
+      // get the template path so we can put it in an admin message box
+      $path = '';
+      if (!array_key_exists('#tripal_template_show', $build[$key]) or 
+           $build[$key]['#tripal_template_show'] == TRUE) {
+        if ($cache and array_key_exists($key, $cache->data) and array_key_exists('path', $cache->data[$key])) {
+
+          $path = $cache->data[$key]['path'] . '/' . $key . '.tpl.php';
+
+          $path = tripal_set_message("Administrators, you can
+            customize the way the content above is presented.  Tripal provides a template
+            file for each block of content.  To customize, copy the template file to your
+            site's default theme, edit then " .
+            l('clear the Drupal cache', 'admin/config/development/performance', array('attributes' => array('target' => '_blank'))) . ".
+            Currently, the content above is provided by this template: <br><br>$path",
+            TRIPAL_INFO,
+            array('return_html' => 1)
+          );
         }
+      }
 
-        //-----------------------
-        // SET THE WEIGHTS FOR THE TOC ELEMENTS
-        //-----------------------
-        // set the weight of the TOC item and add it to our $toc array
-        // for building of the TOC below
-        $weight = 0;
-        if (array_key_exists('#weight', $build[$key])) {
-          $weight = $build[$key]['#weight'];
-        }
-        $toc[$weight][$toc_item_title] = $toc_item_link;
-
-        //-----------------------
-        // CREATE THE DATA BLOCK
-        //-----------------------
-        // add a surrounding <div> box around the content
-        $updated_markup = "
-          <div id=\"$toc_item_id-tripal-data-block\" class=\"tripal-data-block\">
-            <div class=\"$toc_item_id-tripal-data-block-title tripal-data-block-title\">$toc_item_title</div>
-              $markup
-              $path
-            </div>
+      //-----------------------
+      // SET THE WEIGHTS FOR THE TOC ELEMENTS
+      //-----------------------
+      // set the weight of the TOC item and add it to our $toc array
+      // for building of the TOC below
+      $weight = 0;
+      if (array_key_exists('#weight', $build[$key])) {
+        $weight = $build[$key]['#weight'];
+      }
+      $toc[$weight][$toc_item_title] = $toc_item_link;
+
+      //-----------------------
+      // CREATE THE DATA BLOCK
+      //-----------------------
+      // add a surrounding <div> box around the content
+      $updated_markup = "
+        <div id=\"$toc_item_id-tripal-data-block\" class=\"tripal-data-block\">
+          <div class=\"$toc_item_id-tripal-data-block-title tripal-data-block-title\">$toc_item_title</div>
+            $markup
+            $path
           </div>
-        ";
+        </div>
+      ";
 
-        $build[$key]['#markup'] = $updated_markup;
-        $build[$key]['#weight'] = $weight;
-      }
-    }
-  }
+      $build[$key]['#markup'] = $updated_markup;
+      $build[$key]['#weight'] = $weight;
+    } // end foreach ($build as $key => $value) {
+  } // end if ($build['#tripal_generic_node_template'] == TRUE) {
 
   //-----------------------
   // BUILD THE TABLE OF CONTENTS LINKS
@@ -680,7 +738,6 @@ function tripal_core_node_view_alter(&$build) {
     }
   }
   $build['tripal_toc']['#markup'] = "<div id=\"$node->type-tripal-toc-block\" class=\"tripal-toc-block\">$toc_html</div>";
-
 }
 
 /**

tripal_example/theme/templates/tripal_example_teaser.tpl.php

@@ -11,4 +11,4 @@ $example  = $variables['node']->example; ?>
       print "... " . l("[more]", "node/$node->nid");
     } ?>
   </div>
-</div> <?php 
+</div>

tripal_feature/includes/tripal_feature.gff_loader.inc

@@ -974,17 +974,41 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
  */
 function tripal_feature_load_gff3_derives_from($feature, $subject, $organism) {
 
-  // get the subject type
+  // get the subject. If the subject is not in the tripal_gff_temp table
+  // then look for the subject in the feature table using the unique name.
+  // if it is not unique then we can provide an error
   $values = array(
     'organism_id' => $organism->organism_id,
     'uniquename' => $subject,
   );
-  $result = chado_select_record('tripal_gff_temp', array('type_name'), $values);
-  if (count($result) == 0) {
-    tripal_report_error("T_gff3_loader", TRIPAL_WARNING, "Cannot find subject type for feature in 'derives_from' relationship: %subject", array('%subject' => $subject));
-     return '';
+  $result = tripal_core_chado_select('tripal_gff_temp', array('type_name'), $values);
+  $type_id = array();
+  if (count($result) > 0) {
+    $type_id = array(
+      'name' => $result[0]->type_name,
+      'cv_id' => array(
+        'name' => 'sequence'
+      ),
+    );
+  }
+  
+  // if we don't have a subject type then look for the feature in the feature table
+  if (empty($type_id)) {
+    $result = tripal_core_chado_select('feature', array('type_id'), $values);
+    if (count($result) > 1) {
+      watchdog("T_gff3_loader", "Cannot find subject type for feature,'%subject' , in 'derives_from' relationship. Multiple matching features exist with this uniquename.", 
+        array('%subject' => $subject), WATCHDOG_WARNING);
+      return '';
+    }
+    else if (count($result) == 0) {
+      watchdog("T_gff3_loader", "Cannot find subject type for feature,'%subject' , in 'derives_from' relationship.",
+        array('%subject' => $subject), WATCHDOG_WARNING);
+      return '';
+    }
+    else {
+      $type_id = $result->type_id;
+    }
   }
-  $subject_type = $result[0]->type_name;
 
   // get the subject feature
   $match = array(