Filters resultset to match stock id

includes/TripalFields/ncit__raw_data/ncit__raw_data_formatter.inc

@@ -92,7 +92,7 @@ class ncit__raw_data_formatter extends TripalFieldFormatter {
         foreach($germplasm_raw_phenotypes['traits'] as $trait => $exp_loc) {
           list($trait_id, $trait_name) = explode('_', $trait);
 
-          $select = $this->create_select($exp_loc, $germplasm_raw_phenotypes['user']['experiments']);
+          $select = $this->create_select($germplasm_raw_phenotypes['germplasm']['id'], $exp_loc, $germplasm_raw_phenotypes['user']['experiments']);
           $table_row[ $id ] = array(sprintf($icon_img, '', $germplasm_raw_phenotypes['icons']['leaf']) . ucfirst($trait_name), $select, sprintf($icon_img, $trait_id, $germplasm_raw_phenotypes['icons']['export'])); 
           $id++;
         }
@@ -126,20 +126,20 @@ class ncit__raw_data_formatter extends TripalFieldFormatter {
   /**
    * Create select field.
    * 
-   * @param $id
-   *   Id attribute of the final select field.
+   * @param $germplasm
+   *   Stock id number.
    * @param $items
    *   Associative array, where each item will be rendered as an option
    *   with key as the value and value as text.
    * @param $disable
    *   Array of items to match an item if it should be disabled.
    */
-  public function create_select($items, $disable) {
+  public function create_select($germplasm, $items, $disable) {
     $option = array();
     $cache_exp = [];
     foreach($items as $loc_exp) {
       list($trait_id, $project_id, $project_name, $location) = explode('#', $loc_exp);
-      $select_value = $trait_id . '#' . $project_id . '#' . $location;
+      $select_value = $trait_id . '#' . $project_id . '#' . $location . '#' . $germplasm;
       $cache_exp[] = $project_id;
 
       $disabled = (in_array($project_id, $disable)) ? '' : 'disabled';

includes/rawpheno.download.form.inc

@@ -37,10 +37,11 @@ function rawpheno_download($form, &$form_state) {
       if (in_array($param_experiment, $user_experiment)) {
         $param_location = $query_vars['l'];
         $param_trait = (int) $query_vars['t'];
+        $param_stock = (int) $query_vars['g'];
 
         if ($param_experiment > 0 && $param_location && $param_trait > 0) {
           // Create query string.
-          $query_string = 'p=' . $param_experiment . '&l=' . $param_location . '&t=' . $param_trait . '&r=0&e=0&file=0';
+          $query_string = 'p=' . $param_experiment . '&l=' . $param_location . '&t=' . $param_trait . '&r=0&e=0&file=0&g=' . $param_stock;
           drupal_goto('/phenotypes/raw/csv', array('query' => array('code' => base64_encode($query_string))));
         }
       }
@@ -390,7 +391,7 @@ function rawpheno_download_submit($form, &$form_state) {
 
   // Contain all query parameters/string into one string.
   // Decode first when reading this string using base64_decode() function.
-  $url = 'p=' . $prj . '&l=' . $loc . '&t=' . $trt . '&r=' . $rvr . '&e=' . $env . '&file=' . $env_filename;
+  $url = 'p=' . $prj . '&l=' . $loc . '&t=' . $trt . '&r=' . $rvr . '&e=' . $env . '&file=' . $env_filename . '&g=0'; 
 
   // Format url for redirect.
   $form_state['redirect'] = array(

includes/rawpheno.tripaldownload.inc

@@ -209,7 +209,7 @@ function rawpheno_trpdownload_generate_file($variables, $job_id = NULL) {
   }
 
   $q = base64_decode($code);
-  list($project, $location, $traits, $r_version,,) = explode('&', $q);
+  list($project, $location, $traits, $r_version,,,$germplasm) = explode('&', $q);
 
   // Projects:
   $tmp = trim(str_replace('p=', '', $project));
@@ -261,14 +261,30 @@ function rawpheno_trpdownload_generate_file($variables, $job_id = NULL) {
     }
   }
 
-  // Sub-query to select plant_id given a location and project.
-  // NOTE: leading and trailing spaces are required.
-  $sub_sql = " (SELECT plant_id
+  // Germplasm/Stock id - request from germplasm field.
+  $germplasm = trim(str_replace('g=', '', $germplasm));
+
+  if ($germplasm != '' && $gemplasm > 0) {
+    // Sub-query to select plant_id given a location and project and germplasm.
+    // NOTE: leading and trailing spaces are required.
+    $sub_sql = " (SELECT plant_id
+                FROM {pheno_plantprop} INNER JOIN {pheno_plant_project} USING(plant_id)
+                WHERE value IN (:location) AND project_id IN (:project)) 
+                AND plant_id IN (SELECT plant_id FROM pheno_plant WHERE stock_id = :stock_id) ";
+
+    // Query values required by sub query.
+    $arr_q_string = array(':project' => $project, ':location' => $location, ':traits' => $traits, ':stock_id' => $germplasm);
+  }
+  else {
+    // Sub-query to select plant_id given a location and project.
+    // NOTE: leading and trailing spaces are required.
+    $sub_sql = " (SELECT plant_id
                 FROM {pheno_plantprop} INNER JOIN {pheno_plant_project} USING(plant_id)
                 WHERE value IN (:location) AND project_id IN (:project)) ";
 
-  // Query values required by sub query.
-  $arr_q_string = array(':project' => $project, ':location' => $location, ':traits' => $traits);
+    // Query values required by sub query.
+    $arr_q_string = array(':project' => $project, ':location' => $location, ':traits' => $traits);
+  }
 
   // First we need to get the header. This will allow us to ensure that the data
   // downloaded all matches up with the trait it is associated with. Furthermore,

theme/js/rawpheno.germplasm.field.js

@@ -49,7 +49,7 @@
           imgOpacity = '1';
           var params = selectValue.split('#');
           // Project id & location & trait.
-          downloadLink = 'p=' + params[1] + '&l=' + params[2] + '&t=' + params[0];
+          downloadLink = 't=' + params[0] + '&p=' + params[1] + '&l=' + params[2] + '&g=' + params[3];
         }
 
         $('#' + selectId + '-img').css('opacity', imgOpacity);