Added missing files to example module. Working on default CV form

tripal_cv/api/tripal_cv.api.inc

@@ -127,7 +127,7 @@ function tripal_get_cv($identifiers, $options = array()) {
  */
 function tripal_get_cv_select_options() {
 
-  $results = chado_select_record('cv', array('cv_id', 'name'), array());
+  $results = chado_select_record('cv', array('cv_id', 'name'), array(), array('order_by' => array('name' => 'ASC')));
 
   $options = array();
   foreach ($results as $r) {

tripal_cv/includes/tripal_cv.admin.inc

@@ -52,8 +52,123 @@ function tripal_cv_admin_set_defaults_form() {
   $form = array();
   
   $form['instructions'] = array(
-    '#markup' => 'use the following...'
+    '#markup' => t('Much of the data housed in Chado is typed, meaning that a ' .
+        'controlled vocabulary describes what type of data the record is. For example, '.
+        'a feature must have a "type" which is typically a term from ' .
+        'the Sequence Ontology. Record properties typically have a type as well. '.
+        'Tripal allows the administrator to set a default type for each table in '.
+        'Chado that requires a type from a vocabulary. By default, autocomplete fields, '.
+        'type select boxes and type validation occur using the default vocabularies set below. '),
   );
   
+  // get the list of all tables that use the cvterm table as an FK
+  $cvterm_schema = chado_get_schema('cvterm');
+  $referring_tables = $cvterm_schema['referring_tables'];
+  
+  // get the list of tables that already have default set
+  $cv_defaults = db_select('tripal_cv_defaults', 'TCD')
+    ->fields('TCD', array('cv_default_id', 'table_name', 'field_name', 'cv_id'))
+    ->orderBy('table_name', 'ASC')
+    ->execute();
+  
+  // get the list of vocabularies
+  $cvs = tripal_get_cv_select_options();
+  
+  $form['settings'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Configured Defaults'),
+    '#description' => t('The following tables have a default vocabulary'),
+    '#tree' => TRUE,
+  );
+  foreach ($cv_defaults as $cv_default) {
+    $cv_default_id = $cv_default->cv_default_id;
+    $cv = tripal_get_cv(array('cv_id' => $cv_default->cv_id));
+    $form['settings']['existing'][$cv_default_id]["id"] = array(
+      '#type' => 'hidden',
+      '#value' => $cv_default_id,
+    );
+    $form['settings']['existing'][$cv_default_id]["table_name"] = array(
+      '#type' => 'markup',
+      '#markup' => $cv_default->table_name
+    );
+    $form['settings']['existing'][$cv_default_id]["field_name"] = array(
+      '#type' => 'markup',
+      '#markup' => $cv_default->field_name
+    );
+    $form['settings']['existing'][$cv_default_id]["vocabulary"] = array(
+      '#type' => 'select',
+      '#options' => $cvs,
+      '#default_value' => $cv_default->cv_id,
+      '#suffix' => '<a target="_blank" href="'. url('admin/tripal/chado/tripal_cv/cvterms') . '?cv=' . $cv->name . '">View terms</a>'
+    );
+    // remove button
+    $form['settings']['existing'][$cv_default_id]['remove'] = array(
+      '#type' => 'submit',
+      '#value' => t('Remove'),
+      '#name' => "cv_remove-$cv_default_id",
+      '#ajax' => array(
+        'callback' => "tripal_cv_admin_set_defaults_ajax_update",
+        'wrapper' => 'tripal-generic-edit-properties-table',
+        'effect'   => 'fade',
+        'method'   => 'replace',
+        'prevent'  => 'click'
+      ),
+      // When this button is clicked, the form will be validated and submitted.
+      // Therefore, we set custom submit and validate functions to override the
+      // default node form submit.  In the validate function we validate only the
+      // property fields and in the submit we remove the indicated property
+      // from the chado_properties array. In order to keep validate errors
+      // from the node form validate and Drupal required errors for non-property fields
+      // preventing the user from removing properties we set the #limit_validation_errors below
+      '#validate' => array('chado_add_node_form_properties_remove_button_validate'),
+      '#submit' => array('chado_add_node_form_properties_remove_button_submit'),
+      // Limit the validation of the form upon clicking this button to the property_table tree
+      // No other fields will be validated (ie: no fields from the main form or any other api
+      // added form).
+      '#limit_validation_errors' => array(
+        array('property_table')  // Validate all fields within $form_state['values']['property_table']
+      )
+    );
+  }
+  
   return $form;
+}
+
+/**
+ * 
+ * @param unknown $variables
+ */
+function theme_tripal_cv_admin_set_defaults_form($variables) {
+  $element = $variables['element'];
+
+  $header = array(
+    'table_name'      => array('data' => t('Table Name'),      'width' => '20%'),
+    'field_name'      => array('data' => t('Field Name'),      'width' => '20%'),
+    'vocabulary'      => array('data' => t('Default Vocabulary'), 'width' => '40%'),
+    'property_action' => array('data' => t('Actions'),    'width' => '20%'),
+  );
+
+  $rows = array();
+  
+  foreach ($element['settings']['existing'] as $key => $value) {
+    if (is_numeric($key)) {
+      $rows[] = array(
+        drupal_render($value['table_name']),
+        drupal_render($value['field_name']),
+        drupal_render($value['vocabulary']),
+        drupal_render($value['remove']),
+      );
+    }
+  } 
+  $settings_table = theme('table', array(
+    'header' => $header,
+    'rows' => $rows
+  ));
+  $element['settings']['existing'] = array(
+    '#type' => 'markup',
+    '#markup' => $settings_table,
+  );
+  
+  return drupal_render_children($element);
+  
 }

tripal_cv/tripal_cv.module

@@ -326,7 +326,12 @@ function tripal_cv_theme($existing, $type, $theme, $path) {
       'template' => 'tripal_cv_help',
       'variables' =>  array(NULL),
       'path' => "$path/theme/templates"
-    )
+    ),
+    // Default CV form
+    'tripal_cv_admin_set_defaults_form' => array(
+      'function' => 'theme_tripal_cv_admin_set_defaults_form',
+      'render element' => 'element',
+    ),
   );
 
   return $items;

tripal_example/theme/js/tripal_example.js

@@ -0,0 +1,9 @@
+(function($) {
+  Drupal.behaviors.tripal_exampleBehavior = {
+    attach: function (context, settings){
+
+      // Place JavaScript code here
+
+    }
+  };
+})(jQuery);

tripal_example/theme/templates/tripal_example_teaser.tpl.php

@@ -0,0 +1,14 @@
+<?php
+$example  = $variables['node']->example; ?>
+
+<div class="tripal_example-teaser tripal-teaser"> 
+  <div class="tripal-example-teaser-title tripal-teaser-title"><?php 
+    print l("<i>$example->uniquename", "node/$node->nid", array('html' => TRUE));?>
+  </div>
+  <div class="tripal-example-teaser-text tripal-teaser-text"> <?php
+    print substr($example->description, 0, 650);
+    if (strlen($example->description) > 650) {
+      print "... " . l("[more]", "node/$node->nid");
+    } ?>
+  </div>
+</div>

tripal_feature/api/tripal_feature.api.inc

@@ -370,6 +370,7 @@ function tripal_get_sequence($feature, $options) {
 
       // get the reverse compliment if feature is on the reverse strand
       $dir = 'forward';
+      $notes = '';
       if ($parent->strand < 0) {
         $seq = tripal_feature_reverse_complement($seq);
         $dir = 'reverse';

tripal_feature/theme/templates/tripal_feature_sequence.tpl.php

@@ -164,16 +164,18 @@ if ($residues or count($featureloc_sequences) > 0) {
         )
     );
     if (count($cds_sequence) > 0) {
-      $list_items[] = '<a href="#coding_' . $attrs['id'] . '">coding sequnece from alignment at  ' . $attrs['location'] . "</a>";
-      $sequences_html .= '<a name="ccoding_' . $attrs['id'] . '"></a>';
-      $sequences_html .= '<div id="coding_' . $attrs['id'] . '" class="tripal_feature-sequence-item">';
-      $sequences_html .= '<p><b>Coding sequence (CDS) from alignment at  ' . $attrs['location'] . '</b></p>';
-      $sequences_html .= '<pre class="tripal_feature-sequence">';
-      $sequences_html .= '>' . tripal_get_fasta_defline($feature, $attrs['featureloc'], 'CDS') . "\n";
-      $sequences_html .= $cds_sequence[0]['residues'];
-      $sequences_html .= '</pre>';
-      $sequences_html .= '<a href="#sequences-top">back to top</a>';
-      $sequences_html .= '</div>';
+      if ($cds_sequence[0]['residues']) {
+        $list_items[] = '<a href="#coding_' . $attrs['id'] . '">coding sequnece from alignment at  ' . $attrs['location'] . "</a>";
+        $sequences_html .= '<a name="ccoding_' . $attrs['id'] . '"></a>';
+        $sequences_html .= '<div id="coding_' . $attrs['id'] . '" class="tripal_feature-sequence-item">';
+        $sequences_html .= '<p><b>Coding sequence (CDS) from alignment at  ' . $attrs['location'] . '</b></p>';
+        $sequences_html .= '<pre class="tripal_feature-sequence">';
+        $sequences_html .= '>' . tripal_get_fasta_defline($feature, $attrs['featureloc'], 'CDS') . "\n";
+        $sequences_html .= $cds_sequence[0]['residues'];
+        $sequences_html .= '</pre>';
+        $sequences_html .= '<a href="#sequences-top">back to top</a>';
+        $sequences_html .= '</div>';
+      }
     }
   } 
   ?>
@@ -199,13 +201,13 @@ if ($residues or count($featureloc_sequences) > 0) {
       <li>This feature has residues stored in the "residues" field of the feature table of Chado.</li>
       <li>This feature has a protein feature associated via the "feature_relationship" table of Chado with a
           relationship of type "derives from" and the protein feature has residues.</li>
-      <li>This feature has one or more CDS feature associated via the "feature_relationship" table of Chado with a
+      <li>This feature has one or more CDS features associated via the "feature_relationship" table of Chado with a
           relationship of type "part of". If the CDS features have residues then those will be concatenated
-          and presented as a feature.</li>
+          and presented as a sequence.</li>
       <li>This feature is aligned to another feature (e.g. scaffold, or chromosome). In this case, the
-          sequence underlying the alignment will be shown</li>
+          sequence underlying the alignment will be shown.</li>
       <li>This feature is aligned to another feature (e.g. scaffold, or chromosome) and this feature has
-          one ore more CDS features associated.  The CDS sequenes underlying the alignment will be
+          one or more CDS features associated.  The CDS sequenes underlying the alignment will be
           shown.</li>
     </ul>
     </p>';