Added props and dbxref templates for organism

tripal_organism/includes/tripal_organism.chado_node.inc

@@ -505,6 +505,16 @@ function tripal_organism_node_view($node, $view_mode, $langcode) {
           '#tripal_toc_title' => 'Overview',
           '#weight' => -100,
         );
+        $node->content['tripal_organism_properties'] = array(
+          '#markup'  => theme('tripal_organism_properties', array('node' => $node)),
+          '#tripal_toc_id'    => 'properties',
+          '#tripal_toc_title' => 'Properties',
+        );
+        $node->content['tripal_organism_references'] = array(
+          '#markup'  => theme('tripal_organism_references', array('node' => $node)),
+          '#tripal_toc_id'    => 'references',
+          '#tripal_toc_title' => 'Cross References',
+        );
       }
       if ($view_mode == 'teaser') {
         $node->content['tripal_organism_teaser'] = array(

tripal_organism/theme/tripal_organism/tripal_organism_properties.tpl.php

@@ -0,0 +1,48 @@
+<?php
+
+$organism = $variables['node']->organism;
+$options = array('return_array' => 1);
+$organism = tripal_core_expand_chado_vars($organism, 'table', 'organismprop', $options);
+$properties = $organism->organismprop;
+
+if(count($properties) > 0){ 
+    
+  // the $headers array is an array of fields to use as the colum headers.
+  // additional documentation can be found here
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $headers = array('Property Name', 'Value');
+  
+  // the $rows array contains an array of rows where each row is an array
+  // of values for each column of the table in that row.  Additional documentation
+  // can be found here:
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $rows = array();
+  
+  foreach ($properties as $property){
+    $property = tripal_core_expand_chado_vars($property,'field','organismprop.value');
+    $rows[] = array(
+      ucfirst(preg_replace('/_/', ' ', $property->type_id->name)),
+      urldecode($property->value)
+    );
+  }
+   
+  // the $table array contains the headers and rows array as well as other
+  // options for controlling the display of the table.  Additional
+  // documentation can be found here:
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $table = array(
+    'header' => $headers,
+    'rows' => $rows,
+    'attributes' => array(
+      'id' => 'tripal_organism-table-properties',
+    ),
+    'sticky' => FALSE,
+    'caption' => '',
+    'colgroups' => array(),
+    'empty' => '',
+  );
+  
+  // once we have our table array structure defined, we call Drupal's theme_table()
+  // function to generate the table.
+  print theme_table($table); 
+}

tripal_organism/theme/tripal_organism/tripal_organism_references.tpl.php

@@ -0,0 +1,80 @@
+<?php
+$organism = $variables['node']->organism;
+$references = array();
+
+// expand the organism object to include the records from the organism_dbxref table
+$options = array('return_array' => 1);
+$organism = tripal_core_expand_chado_vars($organism, 'table', 'organism_dbxref', $options);
+$organism_dbxrefs = $organism->organism_dbxref;
+if (count($organism_dbxrefs) > 0 ) {
+  foreach ($organism_dbxrefs as $organism_dbxref) {    
+    if($organism_dbxref->dbxref_id->db_id->name == 'GFF_source'){
+      // check to see if the reference 'GFF_source' is there.  This reference is
+      // used to if the Chado Perl GFF loader was used to load the organisms   
+    }
+    else {
+      $references[] = $organism_dbxref->dbxref_id;
+    }
+  }
+}
+
+
+if(count($references) > 0){ ?>
+  <div class="tripal_organism-info-box-desc tripal-info-box-desc">External references for this organism</div><?php
+   
+  // the $headers array is an array of fields to use as the colum headers.
+  // additional documentation can be found here
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $headers = array('Dababase', 'Accession');
+  
+  // the $rows array contains an array of rows where each row is an array
+  // of values for each column of the table in that row.  Additional documentation
+  // can be found here:
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $rows = array();
+
+  foreach ($references as $dbxref){
+  
+    // skip the GFF_source entry as this is just needed for the GBrowse chado adapter 
+    if ($dbxref->db_id->name == 'GFF_source'){
+       continue;  
+    } 
+    $dbname = $dbxref->db_id->name; 
+    if ($dbxref->db_id->url) { 
+      $dbname = l($dbname, $dbxref->db_id->url, array('attributes' => array('target' => '_blank')));
+    } 
+    
+    $accession = $dbxref->accession; 
+    if ($dbxref->db_id->urlprefix) { 
+      $accession = l($accession, $dbxref->db_id->urlprefix . $dbxref->accession, array('attributes' => array('target' => '_blank')));
+    } 
+    if (property_exists($dbxref, 'is_primary')) {
+      $accession .= " <i>(primary cross-reference)</i>";
+    }
+    $rows[] = array(
+      $dbname,
+      $accession
+    );
+  } 
+  
+  // the $table array contains the headers and rows array as well as other
+  // options for controlling the display of the table.  Additional
+  // documentation can be found here:
+  // https://api.drupal.org/api/drupal/includes%21theme.inc/function/theme_table/7
+  $table = array(
+    'header' => $headers,
+    'rows' => $rows,
+    'attributes' => array(
+      'id' => 'tripal_organism-table-references',
+    ),
+    'sticky' => FALSE,
+    'caption' => '',
+    'colgroups' => array(),
+    'empty' => '',
+  );
+  
+  // once we have our table array structure defined, we call Drupal's theme_table()
+  // function to generate the table.
+  print theme_table($table); 
+}?>
+

tripal_organism/tripal_organism.module

@@ -151,6 +151,16 @@ function tripal_organism_theme($existing, $type, $theme, $path) {
       'template' => 'tripal_organism_base',
       'path' => "$path/theme/tripal_organism",
     ),
+    'tripal_organism_properties' => array(
+      'variables' => array('node' => NULL),
+      'template' => 'tripal_organism_properties',
+      'path' => "$path/theme/tripal_organism",
+    ),
+    'tripal_organism_references' => array(
+      'variables' => array('node' => NULL),
+      'template' => 'tripal_organism_references',
+      'path' => "$path/theme/tripal_organism",
+    ),
     'tripal_organism_teaser' => array(
       'variables' => array('node' => NULL),
       'template' => 'tripal_organism_teaser',