Merge pull request #7 from statonlab/master

Fix issue with analysis table
tripal · Mar 22, 2017 · 82d58a4 · 82d58a4
2 parents 351d8c8 + a8f3f4a
commit 82d58a4
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Showing 4 changed files with 56 additions and 18 deletions.
diff --git a/includes/feature_heatmap_form.inc b/includes/feature_heatmap_form.inc
@@ -20,21 +20,35 @@ function e($value) {
 function feature_heatmap_form($form, &$form_state) {
   $form['descriptions'] = array(
     '#type' => 'item',
-    '#markup' => t('<b>Feature unique names need to be separated by comma(,).</b>')
+    '#markup' => t(
+      '<b>Feature unique names need to be separated by comma(,).</b>'
+    ),
+  );
+
+  $form['example_button'] = array(
+    '#type' => 'button',
+    '#value' => 'Try an Example',
+    '#attributes' => array(
+      'class' => array('pull-right', 'btn-info'),
+    ),
   );
 
   $form['heatmap_feature_uniquename'] = array(
     '#type' => 'textarea',
     '#title' => t('Enter feature unique names'),
-    '#description' => t('<b>Example feature unique names:</b> Juglans_nigra_120313_comp34229_c0_seq1 ,Quercus_rubra_120313_comp31392_c0_seq1, Acer_saccharum_022416_comp57075_c0_seq8, Liquidambar_styraciflua_01052015_comp34573_c0_seq2,Fraxinus_pennsylvanica_120313_comp50845_c0_seq2, Nyssa_sylvatica_10132014_comp27824_c0_seq1, Quercus_rubra_120313_comp13209_c0_seq1'),
+    '#description' => t(
+      '<b>Example feature unique names:</b> Fraxinus_pennsylvanica_120313_comp59663_c0_seq1, Fraxinus_pennsylvanica_120313_comp59663_c0_seq2, Fraxinus_pennsylvanica_120313_comp56723_c0_seq1, Fraxinus_pennsylvanica_120313_comp60325_c0_seq16, Fraxinus_pennsylvanica_120313_comp61194_c0_seq4, Fraxinus_pennsylvanica_120313_comp61194_c0_seq5, Fraxinus_pennsylvanica_120313_comp61194_c0_seq8, Fraxinus_pennsylvanica_120313_comp61194_c0_seq6'
+    ),
     '#attributes' => array(
-      'placeholder' => t('Nyssa_sylvatica_10132014_comp23154_c0_seq12_m.8255, Quercus_rubra_120313_comp172643_c0_seq1_m.37896, Liriodendron_tulipifera_10132014_comp16064_c0_seq1'),
+      'placeholder' => 'Example: Fraxinus_pennsylvanica_120313_comp59663_c0_seq1, Fraxinus_pennsylvanica_120313_comp59663_c0_seq2, Fraxinus_pennsylvanica_120313_comp56723_c0_seq1, Fraxinus_pennsylvanica_120313_comp60325_c0_seq16, Fraxinus_pennsylvanica_120313_comp61194_c0_seq4, Fraxinus_pennsylvanica_120313_comp61194_c0_seq5, Fraxinus_pennsylvanica_120313_comp61194_c0_seq8, Fraxinus_pennsylvanica_120313_comp61194_c0_seq6',
     ),
   );
 
   // Escaped get value if it exists
   if (isset($_GET['heatmap_feature_uniquename']) && !empty($_GET['heatmap_feature_uniquename'])) {
-    $form['heatmap_feature_uniquename']['#value'] = e($_GET['heatmap_feature_uniquename']);
+    $form['heatmap_feature_uniquename']['#value'] = e(
+      $_GET['heatmap_feature_uniquename']
+    );
   }
 
 
@@ -60,13 +74,12 @@ function feature_heatmap_form_submit($form, &$form_state) {
 function generate_heatmap_values() {
   // Escaped get value if it exists
   if (!isset($_GET['heatmap_feature_uniquename']) || empty($_GET['heatmap_feature_uniquename'])) {
-    return null;
+    return NULL;
   }
 
   $heatmap_feature_uniquename = e($_GET['heatmap_feature_uniquename']);
 
-  $sql_feature_uniquename =
-    "SELECT ER.elementresult_id, ER.signal, F.feature_id, F.uniquename, 
+  $sql_feature_uniquename = "SELECT ER.elementresult_id, ER.signal, F.feature_id, F.uniquename, 
             Q.name AS quantification_name, Q.analysis_id, 
             B.name, B.biomaterial_id, B.description FROM {chado.elementresult} ER
            INNER JOIN {chado.element} E ON E.element_id = ER.element_id
@@ -86,7 +99,10 @@ function generate_heatmap_values() {
     foreach ($feature_ids as $feature_id) {
       // trim white space at the beginning and the end
       $feature_id = trim($feature_id);
-      $expressions[$feature_id] = db_query($sql_feature_uniquename, array(":feature_uniquename" => $feature_id))->fetchAllAssoc('elementresult_id');
+      $expressions[$feature_id] = db_query(
+        $sql_feature_uniquename,
+        array(":feature_uniquename" => $feature_id)
+      )->fetchAllAssoc('elementresult_id');
     }
   }
 
@@ -118,14 +134,22 @@ function generate_heatmap_values() {
         $analysis_id = $feature->analysis_id;
         $sql_analysis = "SELECT * FROM chado.analysis WHERE analysis_id=:analysis_id";
         if (!empty($analysis_id)) {
-          $analysis = db_query($sql_analysis, array(':analysis_id' => $analysis_id))->fetchAllAssoc('analysis_id');
+          $analysis = db_query(
+            $sql_analysis,
+            array(':analysis_id' => $analysis_id)
+          )->fetchAllAssoc('analysis_id');
           // analysis page url consists of analysis name, sourcename, program and programversion
-          $analysis_url = $analysis[$analysis_id]->name . ', ' .
-            $analysis[$analysis_id]->sourcename . ' (' .
-            $analysis[$analysis_id]->program . ', ' .
-            $analysis[$analysis_id]->programversion . ')';
-          $analysis_url = preg_replace("/[^A-Za-z0-9 ]/", '', $analysis_url); // remove all non-alphanumeric charaters
-          $analysis_url = preg_replace("/\s/", '-', $analysis_url); // replace ' ' with '-'
+          $analysis_url = $analysis[$analysis_id]->name . ', ' . $analysis[$analysis_id]->sourcename . ' (' . $analysis[$analysis_id]->program . ', ' . $analysis[$analysis_id]->programversion . ')';
+          $analysis_url = preg_replace(
+            "/[^A-Za-z0-9 ]/",
+            '',
+            $analysis_url
+          ); // remove all non-alphanumeric charaters
+          $analysis_url = preg_replace(
+            "/\s/",
+            '-',
+            $analysis_url
+          ); // replace ' ' with '-'
           $analysis_url = 'content/' . strtolower($analysis_url);
         }
         // get treatment
@@ -147,7 +171,7 @@ function generate_heatmap_values() {
           'signal' => (float) $feature->signal,
           'description' => $feature->description,
           'quantification_name' => $treatment,
-          'analysis_url' => $analysis_url
+          'analysis_url' => $analysis_url,
         );
       }
     }
@@ -208,7 +232,7 @@ function generate_heatmap_values() {
     return array(
       'heatmap_data' => $heatmap_data,
       'bottom_margin' => $bottom_margin,
-      'left_margin' => $left_margin
+      'left_margin' => $left_margin,
     );
   }
 

diff --git a/includes/tripal_analysis_expression.chado_node.inc b/includes/tripal_analysis_expression.chado_node.inc
@@ -1479,7 +1479,7 @@ function tripal_analysis_expression_node_insert($node) {
     case 'chado_analysis_expression':
 
       // Find the a analysis_expression and add details.     
-      $analysis_expression_id = chado_get_id_from_nid('analysis', $node->nid, 'chado.analysis');
+      $analysis_expression_id = chado_get_id_from_nid('analysis', $node->nid);
       $values = array('analysis_id' => $analysis_expression_id);
       $analysis_expression = chado_generate_var('analysis', $values);
       $node->analysis_expression = $analysis_expression;

diff --git a/js/example.js b/js/example.js
@@ -0,0 +1,13 @@
+(function($) {
+  Drupal.behaviors.tripal_analysis_expression_example = {
+    attach: function (context, settings) {
+      var example = 'Fraxinus_pennsylvanica_120313_comp59663_c0_seq1, Fraxinus_pennsylvanica_120313_comp59663_c0_seq2, Fraxinus_pennsylvanica_120313_comp56723_c0_seq1, Fraxinus_pennsylvanica_120313_comp60325_c0_seq16, Fraxinus_pennsylvanica_120313_comp61194_c0_seq4, Fraxinus_pennsylvanica_120313_comp61194_c0_seq5, Fraxinus_pennsylvanica_120313_comp61194_c0_seq8, Fraxinus_pennsylvanica_120313_comp61194_c0_seq6';
+      $('#edit-example-button').click(function(e) {
+        e.preventDefault()
+        $(this).val('Creating example heat map. Please wait...')
+        $('#edit-heatmap-feature-uniquename').val(example)
+        $(this).parents('form').submit()
+      })
+    }
+  }
+})(jQuery);
diff --git a/tripal_analysis_expression.module b/tripal_analysis_expression.module
@@ -785,6 +785,7 @@ function tripal_analysis_expression_block_view($delta = ''){
     case 'input_features':
       $block['subject'] = t('Feature Expression');
       $block['content'] = drupal_get_form('feature_heatmap_form');
+      drupal_add_js(drupal_get_path('module', 'tripal_analysis_expression') . '/js/example.js');
       break;
     case 'heatmap_features':
       $heatmap = generate_heatmap_values();