Issue #27 - Search new stock name, ignore column and email support.

include/rawpheno.function.measurements.inc

@@ -1176,6 +1176,51 @@ function rawpheno_function_plot_exists($plot, $project_id) {
 
 
 /**
+ * Function to get stock_id number of a stock name in chado.stock.
+ * NOTE: AGL applies only to when saving data. Validation (germplasm exists)
+ *       is based on stock w/o this token.
+ *
+ * @param $stock_name
+ *   A string, the name of the stock.
+ * @param $project_name
+ *   A string, the name of the project.
+ *
+ * @return
+ *   An integer, the stock id number.
+ */
+function rawpheno_function_getstockid($stock_name, $project_name) {
+  // Calling all modules implementing hook_rawpheno_AGILE_stock_name_alter():
+  drupal_alter('rawpheno_AGILE_stock_name', $stock_name, $project_name);
+
+  // Limit the search to project organism.
+  $result = chado_query(
+    "SELECT stock_id FROM {stock} WHERE name = :name LIMIT 1",
+    array(':name' => $stock_name)
+  );
+
+  return ($result) ? $result->fetchField() : 0;
+}
+
+
+/**
+ * Function: get project name.
+ *
+ * @param $project_id
+ *   An integer value, the project id number.
+ *
+ * @return
+ *   A string value, the name for the project from chado.project table.
+ */
+function rawpheno_function_getproject($project_id) {
+  $result = chado_query("SELECT name FROM {project} WHERE project_id = :project_id LIMIT 1", array(
+    ':project_id' => $project_id,
+  ));
+
+  return ($result) ? $result->fetchField() : 0;
+}
+
+
+/** 
  * Function to get environment data files.
  *
  * @param $project

include/rawpheno.upload.excel.inc

@@ -25,6 +25,9 @@ function rawpheno_load_spreadsheet($project_id, $arr_newheaders, $fid, $plantpro
   $plantprop_headers = unserialize($plantprop_headers);
   $arr_newheaders = unserialize($arr_newheaders);
 
+  // Project name.
+  $project_name = rawpheno_function_getproject($project_id);
+
   // First we load the file.
   $file = file_load($fid);
 
@@ -85,6 +88,13 @@ function rawpheno_load_spreadsheet($project_id, $arr_newheaders, $fid, $plantpro
     // print "\nNow parsing each row and saving it to the database...\nNumber of rows saved: \n";
     $i = 0;
 
+    // Skip columns.
+    $skip = array();
+    // Project name.
+    $project_name = rawpheno_function_getproject($project_id);
+    // Calling all modules implementing hook_rawpheno_ignorecols_valsave_alter():
+    drupal_alter('rawpheno_ignorecols_valsave', $skip, $project_name);
+
     // Each row in the spreadsheet.
     foreach ($xls_obj as $row) {
       // Create progress update by computing the number of rows saved in percent.
@@ -134,9 +144,9 @@ function rawpheno_load_spreadsheet($project_id, $arr_newheaders, $fid, $plantpro
       // Process the name column first since we need a plant_id before we can insert any more data.
       // Name column header goes into pheno_plant.
       // Check if stock name exists.
-      $stock_id = NULL;
-      $r = chado_query('SELECT stock_id FROM {stock} WHERE name=:name', array(':name' => trim($row[$name_index])));
-      if ($r) $stock_id = $r->fetchField();
+      unset($stock_id);
+      $stock_id = rawpheno_function_getstockid(trim($row[$name_index]), $project_name);
+      // print $stock_id . ' -- ' . $row[$name_index] . "\n";
 
       // Determine if name has a stock id number.
       if (isset($stock_id) && $stock_id > 0) {
@@ -226,6 +236,14 @@ function rawpheno_load_spreadsheet($project_id, $arr_newheaders, $fid, $plantpro
       // Read each row and each cell.
       // Each row will be an array where name is always the first element.
       foreach($row as $cell_index => $cell_entry) {
+        // Skip this cell when col from durpal_alter hook matches the col.
+        $h = rawpheno_function_delformat($header[$cell_index]);
+
+        if (count($skip) > 0 && in_array($h, $skip)) {
+          // print 'skipping value : ' . $h . '=' . $cell_entry . "\n";
+          continue;
+        }
+
         // For consistency, convert all variations of not applicable to NA.
         if (is_string($cell_entry) && in_array(strtolower($cell_entry), $not_applicable)) {
           $cell_entry = 'NA';
@@ -312,6 +330,11 @@ function rawpheno_load_spreadsheet($project_id, $arr_newheaders, $fid, $plantpro
           // THE REST OF THE COLUMN HEADERS
           // Everything else into pheno_measurements.
           elseif (!empty($cell_colheader) && $cell_entry != 'NA') {
+            if (in_array($cell_colheader, $skip)) {
+              // print 'skipping header : ' . $cell_colheader . "\n";
+              continue;
+            }
+
             // Get the cvterm_id for the trait measurement.
             $type_id = rawpheno_get_trait_id($cell_colheader);
 
@@ -535,6 +558,13 @@ function rawpheno_validate_excel_file($file, $project_id, $source) {
   // Variations of Not Applicable.
   $not_applicable = array('na', 'n/a', 'n.a.');
 
+  // Skip columns.
+  $skip = array();
+  // Project name.
+  $project_name = rawpheno_function_getproject($project_id);
+  // Calling all modules implementing hook_rawpheno_ignorecols_valsave_alter():
+  drupal_alter('rawpheno_ignorecols_valsave', $skip, $project_name);
+
   // Iterate though each row.
   $num_errored_rows = 0;
   $storage = array();
@@ -557,12 +587,18 @@ function rawpheno_validate_excel_file($file, $project_id, $source) {
         $o = 0;
         foreach ($row as $r) {
           $without_format = rawpheno_function_delformat($r);
+
+          // To maintain index of both cells and header, tag either to skip or process
+          // based on headers in drupal_alter hook.
+          $s = (in_array($without_format, $skip)) ? 1 : 0;
+
           $no_units = rawpheno_get_trait_name($r);
           $header[] = array(
             'no format' => $without_format,
             'original' => $r,
             'units' => rawpheno_function_unit($without_format),
             'no units' => $no_units,
+            'skip' => $s,
           );
 
           // Store index number of Plot trait requirements.
@@ -596,6 +632,7 @@ function rawpheno_validate_excel_file($file, $project_id, $source) {
 
         $row_has_error = FALSE;
         foreach ($row as $column_index => $cell) {
+          if ($header[$column_index]['skip'] == 1) continue;
 
           $column_name = $header[$column_index]['no units'];
           if (empty($column_name)) continue;

include/rawpheno.upload.form.inc

@@ -218,6 +218,7 @@ function rawpheno_upload_form_stage_review(&$form, &$form_state) {
 
   // The project id number the spreadsheet and column headers are specific to.
   $project_id = $form_state['values']['sel_project'];
+  $project_name = rawpheno_function_getproject($project_id);
 
   // FIND NEW HEADERS.
   // First step, determine which headers/traits need to be described.
@@ -230,6 +231,10 @@ function rawpheno_upload_form_stage_review(&$form, &$form_state) {
     // when no project id is selected, user will be stopped and is requested to retry the process.
     if ($file AND !empty($project_id)) {
       $new_header = rawpheno_indicate_new_headers($file, $project_id);
+
+      // Calling all modules implementing hook_rawpheno_AGILE_stock_name_alter():
+      drupal_alter('rawpheno_ignorecols_newcolumn', $new_header, $project_name);
+
       $form_state['multistep_values']['new_headers'] = $new_header;
     }
     else {

include/rawpheno.validation.inc

@@ -232,6 +232,8 @@ function validator_column_exists_validate_header($header, $project_id) {
   $nospace_header = array();
 
   foreach ($header as $h) {
+    if ($h['skip'] == 1) continue;
+
     $delformat_header[] = $h['no units'];
     $nospace_header[] = str_replace(' ','', $h['no format']);
   }
@@ -265,6 +267,8 @@ function validator_column_exists_validate_header($header, $project_id) {
   // or closing paren.
   $invalid_format = array();
   foreach($header as $f) {
+    if ($f['skip'] == 1) continue;
+
     $h = trim(str_replace(array("\n", "\r", "  "), ' ', $f['original']));
 
     $is_valid = rawpheno_valid_trait_format($h);

rawpheno.module

@@ -326,6 +326,10 @@ function rawpheno_preprocess_rawpheno_upload_form_master(&$variables, $hook) {
   $variables['rel_url'] = url('phenotypes/raw/instructions');
   // Page Title
   $variables['page_title'] = variable_get('rawpheno_upload_title');
+  // Support Email.
+  $support_email = '';
+  drupal_alter('rawpheno_support_email', $support_email);
+  $variables['support_email'] = $support_email;
 
   // Needs url in help window and links in stage 3.
   $variables['page_url'] =
@@ -334,7 +338,8 @@ function rawpheno_preprocess_rawpheno_upload_form_master(&$variables, $hook) {
       'rawpheno_download'     => url('phenotypes/raw/download'),
       'rawpheno_instructions' => url('phenotypes/raw/instructions'),
       'rawpheno_upload'       => url('phenotypes/raw/upload'),
-      'rawpheno_backup'       => url('phenotypes/raw/backup')
+      'rawpheno_backup'       => url('phenotypes/raw/backup'),
+      'rawpheno_demo'         => url('phenotypes/raw/videos'),
     );
 
   // Stages in upload page.
@@ -1106,11 +1111,15 @@ function rawpheno_block_view($delta = '') {
       $u = explode('.', $url);
       $hostname = (empty($u[0])) ? $url : ucfirst($u[0]);
 
+      $support_email = '';
+      drupal_alter('rawpheno_support_email', $support_email);
+
       $content = theme('rawpheno_notification_block', array(
         'alert' => $alert,
         'username' => $user,
         'hostname' => $hostname,
         'file_count' => $file_count,
+        'support_email' => $support_email,
         'path_module' => base_path() . $path . '/',
         'path_phenotypes_raw' => $GLOBALS['base_url'] . '/phenotypes/raw/',
         'path_phenotypes_video' => file_create_url('public://') . 'tutorial_files/rawpheno_videos/',

theme/css/rawpheno.notification.block.style.css

@@ -196,6 +196,13 @@
   font-size: 1em;
 }
 
+#rawpheno-notification-helptopic-select {
+  font-size: 1em;
+  margin: 2px 0 10px 0;
+  padding: 5px;
+  width: 90%;
+}
+
 /* Media query - apply stype when viewport is 1500px */
 @media(max-width: 1500px) {
   #rawpheno-notification-block-wrapper {

theme/js/rawpheno.notification.block.script.js

@@ -45,6 +45,18 @@
 
         whyBackupInfo.slideUp().hide();
       });
+
+      // Convert help topic select box to a jump menu.
+      if ($('#rawpheno-notification-helptopic-select').length) {
+        $('#rawpheno-notification-helptopic-select').change(function() {
+          var url = $(this).attr('value');
+
+          if (url) {
+            window.open(url, '_blank');
+          }
+        });
+      }
+
     }
   };
 }(jQuery));

theme/js/rawpheno.upload.script.js

@@ -26,6 +26,12 @@
       collapseLink.once(function() {
         $(this).click(function(event) {
           event.preventDefault();
+
+          // Check if select project message is on.
+          if (!$('#float-text').is(':hidden')) {
+            $('#float-text').hide();
+          }
+
           if (helpWindow.is(':hidden')) {
             helpWindow.slideDown(speed, function() {
               collapseLink.text('Close window');

theme/rawpheno_notification_block.tpl.php

@@ -68,12 +68,19 @@
   <div class="rawpheno-notification-item rawpheno-item-c" title="Raw Phenotypes Help Topics">
     <div class="rawpheno-item-wrapper">
       <h3>Need Help? Select a topic below.</h3>
-      <ul>
-        <li><a href="<?php print $path_phenotypes_video . 'rawpheno_backup.mp4'; ?>" target="_blank" class="rawpheno-notification-arrow-right">How to Backup Data Collection Spreadsheet File</a></li>
-        <li><a href="<?php print $path_phenotypes_video . 'rawpheno_upload.mp4'; ?>" target="_blank" class="rawpheno-notification-arrow-right">How to Upload Data to <?php print $hostname; ?></a></li>
-        <li><a href="<?php print $path_phenotypes_raw   . 'instructions'; ?>" target="_blank" class="rawpheno-notification-arrow-right">Standard Phenotyping Procedure</a></li>
-        <li><a href="<?php print $path_phenotypes_raw   . 'videos'; ?>" target="_blank" class="rawpheno-notification-arrow-right">Other Video Demonstrations</a></li>
-      </ul>
+
+      <select id="rawpheno-notification-helptopic-select">
+        <option value="">---</option>
+        <option value="<?php print $path_phenotypes_video . 'rawpheno_backup.mp4'; ?>">How to Backup Spreadsheet File</option>
+        <option value="<?php print $path_phenotypes_video . 'rawpheno_upload.mp4'; ?>">How to Upload Data to <?php print $hostname; ?></option>
+        <option value="<?php print $path_phenotypes_raw   . 'instructions';        ?>">Standard Phenotyping Procedure</option>
+        <option value="<?php print $path_phenotypes_raw   . 'videos';              ?>">Other Video Demonstrations</option>
+      </select>
+
+      <?php if (isset($support_email) && !empty($support_email)) { ?>
+        <h3>Still need a help? Send us an email.</h3>
+        <span class="rawpheno-notification-arrow-right">Email: <a href="mailto:<?php print $support_email; ?>">KnowPulse Support</a></span>
+      <?php } ?>
     </div>
   </div>
 </div>

theme/rawpheno_pages.tpl.php

@@ -249,6 +249,16 @@
                   <a href="<?php print $page_url['rawpheno_download'] ?>" target="_blank">downloads</a></em>.
                 </li>
               </ul>
+
+              <br />
+              <div>
+                <h3>&bull; Still Need Help?</h3>
+                <a href="<?php print $page_url['rawpheno_demo'] ?>" title="This link opens a new window" target="_blank">Watch Raw Phenotypes Video Demonstrations</a>
+
+                <?php if (isset($support_email) && !empty($support_email)) { ?>
+                or Send Us an Email: <a href="mailto:<?php print $support_email; ?>" title="Right click to copy email address">KnowPulse Support</a></span>
+                <?php } ?>
+              </div>
             </div>
 
             <div>