Streamlined the code for the feature admin summart chart and added extensive commenting to make it easier to create similar charts for other admin pages in the future.

tripal_feature/includes/tripal_feature.admin.inc

@@ -37,61 +37,70 @@ function tripal_feature_admin_feature_view() {
   }
 
   // Add a summary chart.
+  //-----------------------------------
+  // We are using the organism_feature_count materialized view as the source for our data.
+  // Thus grab all the records from this materialized view.
   $organism_feature_count = chado_select_record(
     'organism_feature_count',
     array('*'),
     array(),
     array('order_by' => array('genus' => 'ASC', 'species' => 'ASC', 'feature_type' => 'ASC', 'num_features' => 'DESC'))
   );
-  $summary = array();
-  $organisms = array();
-  $types = array();
+
+  // Initialize variables.
   $chart = array();
+  $type_names = array();
+  $organism_names = array();
+
+  // Process each row of the materialzied view into the chart array.
+  // Note: it's first keyed by type since each type will be a bar. Each type will have
+  // a "bars" array with the start (y0) and end (y1) height on the bar for a given
+  // organism. Finally we keep a record of the names of the types & organisms
+  // for axis' and legend generation respectively.
   foreach ($organism_feature_count as $row) {
 
-    $summary[$row->organism_id][$row->cvterm_id] = $row->num_features;
-
-    $organisms[$row->organism_id]['organism_id'] = $row->organism_id;
-    $organisms[$row->organism_id]['genus'] = $row->genus;
-    $organisms[$row->organism_id]['species'] = $row->species;
-    $organisms[$row->organism_id]['common_name'] = $row->common_name;
-    $organisms[$row->organism_id]['scientific_name'] = $row->genus . ' ' . $row->species;
-    $organisms[$row->organism_id]['total_features'] = (isset($organisms[$row->organism_id]['total_features'])) ? $organisms[$row->organism_id]['total_features'] + $row->num_features : $row->num_features;
-
-    $types[$row->cvterm_id]['cvterm_id'] = $row->cvterm_id;
-    $types[$row->cvterm_id]['name'] = $row->feature_type;
-    $types[$row->cvterm_id]['total_features'] = (isset($types[$row->cvterm_id]['total_features'])) ? $types[$row->cvterm_id]['total_features'] + $row->num_features : $row->num_features;
-
-
+    // Build up the easy details for the current row's type. These will be overridden
+    // multiple times but that's more efficient than checking each time.
     $chart[$row->cvterm_id]['cvterm_id'] = $row->cvterm_id;
     $chart[$row->cvterm_id]['name'] = $row->feature_type;
-    $chart[$row->cvterm_id]['max_features'] = (isset($types[$row->cvterm_id]['max_features'])) ? max($types[$row->cvterm_id]['max_features'], $row->num_features) : $row->num_features;
+
+    // Save the name of the type and organism into their respective arrays
+    // for generation of axis' and legends for the chart.
+    $type_names[$row->cvterm_id] = $row->feature_type;
+    $organism_names[$row->organism_id] = $row->genus . ' ' . $row->species;
+
+    // Save information about the current organism. This isn't actually used by the
+    // chart but can be used to debug the bar generation to follow.
     $chart[$row->cvterm_id]['organisms'][] = array(
       'name' => $row->genus . ' ' . $row->species,
       'value' => (int) $row->num_features
     );
-    $type_names[$row->cvterm_id] = $row->feature_type;
-    $organism_names[$row->organism_id] = $row->genus . ' ' . $row->species;
-  }
 
-  // Quick processing of the organisms array per type
-  // to build-up the stacked bars.
-  foreach ($chart as $type_id => $bar) {
-    $y0 = 0;
-    $y1 = 0;
-    $chart[$type_id]['bars'] = array();
-    foreach ($bar['organisms'] as $k => $org) {
-      $y0 = $y1;
-      $y1 = $y0 + $org['value'];
-      $chart[$type_id]['bars'][$k]['name'] = $org['name'];
-      $chart[$type_id]['bars'][$k]['y0'] = $y0;
-      $chart[$type_id]['bars'][$k]['y1'] = $y1;
+    // Now to build the bar array with the start (y0) and end (y1) height on the
+    // bar for a given organism.
+    // NOTE: we cannot assume the types are all in order so store y0 & y1 in the
+    // $chart[type] array.
+    // If y0 has not yet been set for this type then we're starting with the first
+    // chunk (organism) on the bar.
+    if (!isset($chart[$row->cvterm_id]['y0'])) {
+      $chart[$row->cvterm_id]['y0'] = 0;
+      $chart[$row->cvterm_id]['y1'] = $row->num_features;
     }
-    $chart[$type_id]['total_features'] = $y1;
-  }
+    // Otherwise, add the next chunk (organism) on top of the pre-existing bar.
+    else {
+      $chart[$row->cvterm_id]['y0'] = $chart[$row->cvterm_id]['y1'];
+      $chart[$row->cvterm_id]['y1'] = $chart[$row->cvterm_id]['y0'] + $row->num_features;
+    }
+    // Now save the bar chunk we just determined.
+    $chart[$row->cvterm_id]['bars'][] = array(
+      'name' => $row->genus . ' ' . $row->species,
+      'y0' => $chart[$row->cvterm_id]['y0'],
+      'y1' => $chart[$row->cvterm_id]['y1'],
+    );
 
-  $variables['organisms'] = $organisms;
-  $variables['types'] = $types;
+    // We also need to keep track of the total number of features for a single bar (Type).
+    $chart[$row->cvterm_id]['total_features'] = $chart[$row->cvterm_id]['y1'];
+  }
 
   // Sort based on the total number of features.
   // NOTE: This changes the keys so it's no longer the organism/type_id.
@@ -108,9 +117,8 @@ function tripal_feature_admin_feature_view() {
     array(':mv_table' => 'organism_feature_count')
   )->fetchObject();
 
-  tripal_add_d3js();
-  drupal_add_css(drupal_get_path('module','tripal_feature') . '/theme/css/tripal_feature.css');
-  drupal_add_js(drupal_get_path('module','tripal_feature') . '/theme/js/tripalFeature.adminChart.js');
+  // Save everything we just determined as a Drupal JS settings so that we have access to
+  // it in our js script.
   drupal_add_js(array('tripalFeature' => array('admin' => array(
     'summary' => $chart,
     'types' => $type_names,
@@ -120,6 +128,10 @@ function tripal_feature_admin_feature_view() {
     'mviewLastUpdate' => format_date($mview->last_update),
   ))), 'setting');
 
+  // Finally add all the javascript and css needed to render the chart.
+  tripal_add_d3js();
+  drupal_add_css(drupal_get_path('module','tripal_feature') . '/theme/css/tripal_feature.css');
+  drupal_add_js(drupal_get_path('module','tripal_feature') . '/theme/js/tripalFeature.adminChart.js');
 
   return $output;
 }