Periodic check-in

tripal/api/tripal.terms.api.inc

@@ -61,43 +61,6 @@ function hook_vocab_storage_info() {
   );
 }
 
-
-/**
- * Creates a form for specifying a term for TripalEntity creation.
- *
- * This hook allows the module that implements a vocabulary storage backend
- * to provide the form necessary to select a term that will then be used for
- * creating a new TripalEntity type.  Tripal will expect that a 'vocabulary' and
- * 'accession' are in the $form_state['storage'] array. The 'vocabulary' and
- * must be the abbreviated uppercase vocabulary for the vocabulary (e.g. 'RO',
- * 'SO', 'PATO', etc.).  The 'accession' must be the unique term ID (or
- * accession) for the term in the vocabulary.
- *
- * @param $form
- * @param $form_state
- *
- * @return
- *   A form object.
- *
- * @ingroup tripal_terms_api
- */
-function hook_vocab_select_term_form(&$form, &$form_state) {
-
-  return $form;
-}
-
-/**
- * Validates the hook_vocab_select_term_form().
- *
- * @param $form
- * @param $form_state
- *
- * @ingroup tripal_terms_api
- */
-function hook_vocab_select_term_form_validate($form, &$form_state) {
-
-}
-
 /**
  * Provides a form for importing vocabularies and their terms.
  *
@@ -618,17 +581,24 @@ function tripal_get_vocabularies() {
  */
 function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
     $title = 'Vocabulary Term', $description = '', $is_required,
-    $field_name = '', $delta = 0 ) {
+    $field_name = '', $delta = 0, $callback = '') {
   
   $ajax_wrapper_id = 'tripal-vocab-select-form-' . $delta;
   if ($field_name) {
     $ajax_wrapper_id = $field_name . '-' . $delta;
   }
+  
+  if (!$callback) {
+    $callback = 'tripal_get_term_lookup_form_ajax_callback';
+  }
 
   $term_name = $default_name;
   if (array_key_exists('values', $form_state) and array_key_exists('term_name', $form_state['values'])) {
     $term_name = $form_state['values']['term_name'];
   }
+  if (array_key_exists('input', $form_state) and array_key_exists('term_name', $form_state['input'])) {
+    $term_name = $form_state['input']['term_name'];
+  }
   if ($field_name and array_key_exists('input', $form_state) and array_key_exists($field_name, $form_state['input'])) {
     $term_name = $form_state['input'][$field_name]['und'][$delta]['term_match']['term_name'];
   }
@@ -642,7 +612,7 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
   $form_state['storage'][$ajax_wrapper_id]['term_match_field'] = $field_name;
   $form_state['storage'][$ajax_wrapper_id]['term_match_delta'] = $delta;
 
-  $form['term_match'] = array(
+  $form['term_match' . $delta] = array(
     '#type' => 'fieldset',
     '#collapsible' => FALSE,
     '#collapsed' => FALSE,
@@ -650,7 +620,7 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
     '#prefix' => '<div id = "' . $ajax_wrapper_id . '">',
     '#suffix' => '</div>',
   );
-  $form['term_match']['term_name'] = array(
+  $form['term_match' . $delta]['term_name' . $delta] = array(
     '#title'  => t('Type'),
     '#type' => 'textfield',
     '#description' => $description,
@@ -658,14 +628,14 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
     '#default_value' => $term_name,
     '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/",
   );
-  $form['term_match']['select_button'] = array(
+  $form['term_match' . $delta]['select_button' . $delta] = array(
     '#type' => 'button',
     '#value' => t('Lookup Term'),
     '#name' => 'select_cvterm_' . $ajax_wrapper_id,
     '#validate' => array(),
     '#limit_validation_errors' => array(),
     '#ajax' => array(
-      'callback' => "tripal_get_term_lookup_form_ajax_callback",
+      'callback' => $callback,
       'wrapper' => $ajax_wrapper_id,
       'effect' => 'fade',
       'method' => 'replace'
@@ -676,12 +646,12 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
   // matching terms in the database and let them select among any matches.
   if ($term_name) {
     $submit_disabled = TRUE;
-    $form['term_match']['terms_list'] = array(
+    $form['term_match' . $delta]['terms_list' . $delta] = array(
       '#type' => 'fieldset',
       '#title' => t('Matching Terms'),
-      '#description' => t('Please select the term the best matches the
-          content type you want to create. If the same term exists in
-          multiple vocabularies you will see more than one option below.')
+      '#description' => t('Please select the best matching term. If the 
+        same term exists in multiple vocabularies you will see more than 
+        one option below.')
     );
     $match = array(
       'name' => $term_name,
@@ -700,23 +670,24 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
     foreach ($terms as $term) {
       // Save the user a click by setting the default value as 1 if there's
       // only one matching term.
-      $default = FALSE;
+      $checked = FALSE;
       $attrs = array();
       if ($num_terms == 0 and count($terms) == 1) {
-        $default = TRUE;
+        $checked = TRUE;
         $attrs = array('checked' => 'checked');
       }
-      $term_element_name = 'term-' . $term->cvterm_id;
-      $form['term_match']['terms_list'][$term_element_name] = array(
+      $term_element_name = 'term-' . $term->cvterm_id  . '-' . $delta;
+      $definition = property_exists($term, 'definition') ? $term->definition : '';
+      $form['term_match' . $delta]['terms_list' . $delta][$term_element_name] = array(
         '#type' => 'checkbox',
         '#title' =>  $term->name,
-        '#default_value' => $default,
+        '#default_value' => $checked,
         '#attributes' => $attrs,
         '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name . ' (' . $term->dbxref_id->db_id->name . ') ' . $term->cv_id->definition .
-        '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
-        '<br><b>Definition:</b>  ' . property_exists($term, 'definition') ? $term->definition : '',
+          '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
+          '<br><b>Definition:</b>  ' . $definition,
         '#ajax' => array(
-          'callback' => "tripal_get_term_lookup_form_ajax_callback",
+          'callback' => $callback,
           'wrapper' => $ajax_wrapper_id,
           'effect' => 'fade',
           'method' => 'replace'
@@ -741,24 +712,25 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
       $term = $synonym->cvterm_id;
       // Save the user a click by setting the default value as 1 if there's
       // only one matching term.
-      $default = FALSE;
+      $checked = FALSE;
       $attrs = array();
       if ($num_terms == 0 and count($terms) == 1) {
-        $default = TRUE;
+        $checked = TRUE;
         $attrs = array('checked' => 'checked');
       }
-      $term_element_name = 'term-' . $term->cvterm_id;
-      $form['term_match']['terms_list'][$term_element_name] = array(
+      $term_element_name = 'term-' . $term->cvterm_id . '-' . $delta;
+      $definition = property_exists($term, 'definition') ? $term->definition : '';
+      $form['term_match' . $delta]['terms_list' . $delta][$term_element_name] = array(
         '#type' => 'checkbox',
         '#title' =>  $term->name,
-        '#default_value' => $default,
+        '#default_value' => $checked,
         '#attributes' => $attrs,
         '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name . ' (' . $term->dbxref_id->db_id->name . ') ' . $term->cv_id->definition .
         '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
-        '<br><b>Definition:</b>  ' . $term->definition . 
+        '<br><b>Definition:</b>  ' . $definition . 
         '<br><b>Synonym:</b> ' . $synonym->synonym,
         '#ajax' => array(
-          'callback' => "tripal_get_term_lookup_form_ajax_callback",
+          'callback' => $callback,
           'wrapper' => $ajax_wrapper_id,
           'effect' => 'fade',
           'method' => 'replace'
@@ -767,14 +739,14 @@ function tripal_get_term_lookup_form(&$form, &$form_state, $default_name = '',
       
       if (array_key_exists('values', $form_state) and array_key_exists($term_element_name, $form_state['values']) and
         $form_state['values'][$term_element_name] == 1) {
-          $selected_term = $term;
-        }
-        $num_terms++;
+        $selected_term = $term;
+      }
+      $num_terms++;
     }
     
     
     if ($num_terms == 0) {
-      $form['term_match']['terms_list']['none'] = array(
+      $form['term_match'. $delta]['terms_list'. $delta]['none'. $delta] = array(
         '#type' => 'item',
         '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
       );
@@ -804,8 +776,8 @@ function tripal_get_term_lookup_form_result($form, $form_state, $field_name = ''
   $values = array();
   $selected = array();
   if ($field_name) {
-    if (array_key_exists('term_match', $form_state['values'][$field_name]['und'][$delta]) and 
-      array_key_exists('terms_list', $form_state['values'][$field_name]['und'][$delta]['term_match'])) {
+    if (array_key_exists('term_match' . $delta, $form_state['values'][$field_name]['und'][$delta]) and 
+        array_key_exists('terms_list' . $delta, $form_state['values'][$field_name]['und'][$delta]['term_match'. $delta])) {
       $values = $form_state['values'][$field_name]['und'][$delta]['term_match']['terms_list'];
     }
   }
@@ -816,7 +788,7 @@ function tripal_get_term_lookup_form_result($form, $form_state, $field_name = ''
   if (is_array($values)) {
     foreach ($values as $key => $value) {
       $matches = array();
-      if (preg_match("/^term-(\d+)$/", $key, $matches) and $values['term-' . $matches[1]]) {
+      if (preg_match("/^term-(\d+)-$delta$/", $key, $matches) and $values['term-' . $matches[1] . '-' . $delta]) {
         $cvterm_id = $matches[1];
         $selected[] = chado_generate_var('cvterm', array('cvterm_id' => $cvterm_id));
       }
@@ -839,9 +811,9 @@ function tripal_get_term_lookup_form_ajax_callback($form, $form_state) {
   // If this form is in a field then we need to dig a bit deeper to return
   // the form elements.
   if ($field_name) {
-    return $form[$field_name]['und'][$delta]['term_match'];
+    return $form[$field_name]['und'][$delta]['term_match'. $delta];
   }
   else {
-    return $form['term_match'];
+    return $form['term_match' . $delta];
   }
 }

tripal/includes/TripalBundleUIController.inc

@@ -537,6 +537,7 @@ function tripal_bundle_access($op, $type = NULL, $account = NULL) {
  */
 function tripal_admin_add_type_form($form, &$form_state) {
 
+  // Make sure we have a storage backend for managing content types.
   $stores = module_invoke_all('vocab_storage_info');
   if (!is_array($stores) or count($stores) == 0) {
     tripal_set_message('A storage backend is not enabled for managing
@@ -545,202 +546,209 @@ function tripal_admin_add_type_form($form, &$form_state) {
           and return to create new Tripal content types.', TRIPAL_NOTICE);
     return;
   }
-  $keys = array_keys($stores);
-  $module = $stores[$keys[0]]['module'];
-  $function = $module . '_vocab_select_term_form';
-  if (function_exists($function)) {
-    $form = $function($form, $form_state);
+  
+  // Set the stage to step1 if it isn't already set.
+  if (!isset($form_state['stage'])) $form_state['stage'] = 'step1';
+  $stage = $form_state['stage'];
+  
+  
+  // Get the selected term.
+  if (array_key_exists('values', $form_state) and
+      array_key_exists('term', $form_state['values'])) {
+    $selected_term = $form_state['values']['term'];
+  }
+  else {
+    $selected = tripal_get_term_lookup_form_result($form, $form_state);
+    $selected_term = $selected[0];
+  }
+    
+  // Get the selected storage element.
+  $default_store = 'term_chado_storage';
+  if (array_key_exists('values', $form_state) and
+      array_key_exists('store_select', $form_state['values'])) {
+    $default_store = $form_state['values']['store_select'];
   }
+  
 
-  $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
+  // Handle the different stages:
+  if ($stage == 'step1') {
+    tripal_admin_add_type_form_step1($form, $form_state);
+  }
+  if ($form_state['stage'] == 'step2') {
+    tripal_admin_add_type_form_step1_summary($form, $form_state, $selected_term);
+    tripal_admin_add_type_form_step2($form, $form_state, $stores, $selected_term, $default_store);
+  }
+  if ($form_state['stage'] == 'step3') {
+    tripal_admin_add_type_form_step1_summary($form, $form_state, $selected_term);
+    tripal_admin_add_type_form_step2_summary($form, $form_state, $stores, $selected_term, $default_store);
+    tripal_admin_add_type_form_step3($form, $form_state, $stores, $selected_term, $default_store);
+  }
+  
+  $form['#prefix'] = '<div id = "tripal-add-type-form">';
+  $form['#suffix'] = '</div>';
+  
+  return $form;
+}
 
-  // If no term has been selected yet then provide the auto complete field.
-  $form['term_name'] = array(
-    '#title'       => t('Content Type'),
-    '#type'        => 'textfield',
-    '#description' => t("The content type must be the name of a term in
+/**
+ * Builds step1 of the tripal_admin_add_type_form()
+ */
+function tripal_admin_add_type_form_step1(&$form, &$form_state) {
+  
+  // Get the term name from the form_state.
+  $term_name = '';
+  if (array_key_exists('values', $form_state) and array_key_exists('term_name0', $form_state['values'])) {
+    $term_name = $form_state['values']['term_name0'];
+  }
+  if (array_key_exists('input', $form_state) and array_key_exists('term_name0', $form_state['input'])) {
+    $term_name = $form_state['input']['term_name0'];
+  }
+  
+  // Get the term lookup form.
+  $description = t("The content type must be the name of a term in
         a controlled vocabulary and the controlled vocabulary should
         already be loaded into Tripal.  For example, to create a content
         type for storing 'genes', use the 'gene' term from the
-        Sequence Ontology (SO)."),
-    '#required'    => TRUE,
-    '#default_value' => $term_name,
-    '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/",
-  );
-  $form['select_button'] = array(
+        Sequence Ontology (SO).");
+  tripal_get_term_lookup_form($form, $form_state, $term_name,
+    'Step 1: Content Type', $description, TRUE, '', 0,
+    'tripal_admin_add_type_form_ajax_callback');
+  
+  if ($term_name) {
+    $form['term_match']['step1-continue'] = array(
+      '#type' => 'submit',
+      '#value' => t('Continue'),
+      '#name' => 'step1-continue',
+    );
+  }
+}
+
+/**
+ * Provides a summary of values selected in Step 1. 
+ */
+function tripal_admin_add_type_form_step1_summary(&$form, &$form_state, $selected_term) {
+     
+  $form['term'] = [
+    '#type' => 'value',
+    '#value' => $selected_term,
+  ];
+  
+  $form['term_summary'] = [
+    '#type' => 'fieldset',
+    '#title' => t('Step 1: Content Type'),
+    '#description' => '',
+    '#collapsible' => TRUE,
+    '#collapsed' => TRUE,
+  ];
+  $definition = property_exists($selected_term, 'definition') ? $selected_term->definition : '';
+  $form['term_summary']['details'] = [
+    '#type' => 'item',
+    '#title' => t('Term'),
+    '#markup' => '<b>Vocabulary:</b> ' . $selected_term->cv_id->name . ' (' . $selected_term->dbxref_id->db_id->name . ') ' . $selected_term->cv_id->definition .
+    '<br><b>Term: </b> ' . $selected_term->dbxref_id->db_id->name . ':' . $selected_term->dbxref_id->accession . '.  ' .
+    '<br><b>Definition:</b>  ' . $definition
+  ];
+  $form['term_summary']['step1-return'] = array(
     '#type' => 'submit',
-    '#value' => t('Lookup Term'),
-    '#name' => 'select_cvterm',
+    '#value' => t('Pick a different term'),
+    '#name' => 'step1-return',
+  );  
+}
+  
+/**
+ * Builds step1 of the tripal_admin_add_type_form()
+ */
+function tripal_admin_add_type_form_step2(&$form, &$form_state, $stores) {
+  
+  // Now let the user select where the data type will be stored.
+  $form['storage'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Step 2: Storage'),
+    '#description' => t('The primary record for each content of this type
+          must be stored in a single storage backend. Please select the
+          storage method and settings for this content type.')
+  );
+    
+  $store_options = array(0 => '-- Select --');
+  foreach ($stores as $store_type => $store) {
+    $store_options[$store_type] = $store['label'];
+  }
+
+  $form['storage']['store_select'] = array(
+    '#type' => 'select',
+    '#title' => 'Storage backend',
+    '#options' => $store_options,
+    '#default_value' => $default_store,
     '#ajax' => array(
       'callback' => "tripal_admin_add_type_form_ajax_callback",
-      'wrapper' => "tripal-vocab-select-form",
+      'wrapper' => "tripal-add-type-form",
       'effect' => 'fade',
       'method' => 'replace'
     ),
+    '#description' => 'Select a storage background for this content type.'
   );
-  $form['#prefix'] = '<div id = "tripal-vocab-select-form">';
-  $form['#suffix'] = '</div>';
-
-  // If the term has been provided by the user then we want to search for
-  // matching terms in the database and let them select among any matches.
-  if ($term_name) {
-    $submit_disabled = TRUE;
-    $form['terms_list'] = array(
-      '#type' => 'fieldset',
-      '#title' => t('Matching Terms'),
-      '#description' => t('Please select the term the best matches the
-          content type you want to create. If the same term exists in
-          multiple vocabularies you will see more than one option below.')
-    );
-    $match = array(
-      'name' => $term_name,
-    );
-    $terms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));
-    $terms = chado_expand_var($terms, 'field', 'cvterm.definition');
-    $num_terms = 0;
-    $selected_term = '';
-
-    // Let the user select from any matching terms. Sometimes there may be
-    // more than one that match.
-    foreach ($terms as $term) {
-      // Save the user a click by setting the default value as 1 if there's
-      // only one matching term. 
-      $default = FALSE;
-      $attrs = array();
-      if ($num_terms == 0 and count($terms) == 1) {
-        $default = TRUE;
-        $attrs = array('checked' => 'checked');
-      }
-      $term_element_name = 'term-' . $term->cvterm_id;
-      $form['terms_list'][$term_element_name] = array(
-        '#type' => 'checkbox',
-        '#title' =>  $term->name,
-        '#default_value' => $default,
-        '#attributes' => $attrs,
-        '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name . ' (' . $term->dbxref_id->db_id->name . ') ' . $term->cv_id->definition .
-        '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
-        '<br><b>Definition:</b>  ' . $term->definition,
-        '#ajax' => array(
-          'callback' => "tripal_admin_add_type_form_ajax_callback",
-          'wrapper' => "tripal-vocab-select-form",
-          'effect' => 'fade',
-          'method' => 'replace'
-        ),
-      );
-
-      if (array_key_exists('values', $form_state) and array_key_exists($term_element_name, $form_state['values']) and
-          $form_state['values'][$term_element_name] == 1) {
-        $selected_term = $term;
-      }
-      $num_terms++;
-    }
-    
-    
-    // Next find terms that are synonyms
-    $match = array(
-      'synonym' => $term_name,
-    );
-    $termsyn = chado_generate_var('cvtermsynonym', $match, array('return_array' => TRUE));
-    // Let the user select from any matching terms. Sometimes there may be
-    // more than one that match.
-    foreach ($termsyn as $synonym) {
-      $term = $synonym->cvterm_id;
-      // Save the user a click by setting the default value as 1 if there's
-      // only one matching term.
-      $default = FALSE;
-      $attrs = array();
-      if ($num_terms == 0 and count($terms) == 1) {
-        $default = TRUE;
-        $attrs = array('checked' => 'checked');
-      }
-      $term_element_name = 'term-' . $term->cvterm_id;
-      $form['term_match']['terms_list'][$term_element_name] = array(
-        '#type' => 'checkbox',
-        '#title' =>  $term->name,
-        '#default_value' => $default,
-        '#attributes' => $attrs,
-        '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name . ' (' . $term->dbxref_id->db_id->name . ') ' . $term->cv_id->definition .
-        '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
-        '<br><b>Definition:</b>  ' . $term->definition .
-        '<br><b>Synonym:</b> ' . $synonym->synonym,
-        '#ajax' => array(
-          'callback' => "tripal_admin_add_type_form_ajax_callback",
-          'wrapper' => "tripal-vocab-select-form",
-          'effect' => 'fade',
-          'method' => 'replace'
-        ),
-      );
-      
-      if (array_key_exists('values', $form_state) and array_key_exists($term_element_name, $form_state['values']) and
-        $form_state['values'][$term_element_name] == 1) {
-          $selected_term = $term;
-        }
-        $num_terms++;
-    }
-    if ($num_terms == 0) {
-      $form['terms_list']['none'] = array(
-        '#type' => 'item',
-        '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
-      );
-      return $form;
-    }
-
-    // Now let the user select where the data type will be stored.
-    $form['storage'] = array(
-      '#type' => 'fieldset',
-      '#title' => t('Storage Settings'),
-      '#description' => t('The primary record for each content of this type
-          must be stored in a single storage backend. Please select the
-          storage method and settings for this content type.')
-    );
-
-    // TODO: there should be a way for each storage backend to determine if
-    // it can handle the content type.  Maybe certain content types aren't
-    // yet supported by every storage backend.
-    $default_store = 'term_chado_storage';
-    $store_options = array(0 => '-- Select --');
-    foreach ($stores as $store_type => $store) {
-      $store_options[$store_type] = $store['label'];
-    }
-    if (array_key_exists('values', $form_state) and
-        array_key_exists('store_select', $form_state['values'])) {
-      $default_store = $form_state['values']['store_select'];
-    }
-    $form['storage']['store_select'] = array(
-      '#type' => 'select',
-      '#title' => 'Storage backend',
-      '#options' => $store_options,
-      '#default_value' => $default_store,
-      '#ajax' => array(
-        'callback' => "tripal_admin_add_type_form_ajax_callback",
-        'wrapper' => "tripal-vocab-select-form",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-      '#description' => 'Select a storage background for this content type.'
+  
+  if ($default_store) {
+    $form['term_match']['step2-continue'] = array(
+      '#type' => 'submit',
+      '#value' => t('Continue'),
+      '#name' => 'step2-continue',
     );
-
-    if ($default_store) {
-      $selected_store_module = $stores[$store_type]['module'];
-
-      $function = $selected_store_module . '_field_storage_bundle_mapping_form';
-      if (function_exists($function)) {
-        $store_form = $function($form, $form_state, $selected_term, $submit_disabled);
-        $form['storage'][$store_type] = $store_form;
-      }
-
-      // Add in the button for the cases of no terms or too many.
-      $form['submit_button'] = array(
-        '#type' => 'submit',
-        '#value' => t('Create content type'),
-        '#name' => 'use_cvterm',
-        '#disabled' => $submit_disabled,
-      );
-    }
   }
+}
 
+/**
+ * Provides a summary of values selected in Step 1.
+ */
+function tripal_admin_add_type_form_step2_summary(&$form, &$form_state, $stores) {
+  $default_store = $form_state['values']['store_select'];
+  $selected_store_module = $stores[$default_store]['module'];
+  
+  $form['store_select'] = [
+    '#type' => 'value',
+    '#value' => $default_store,
+  ];
+  
+  $form['store_summary'] = [
+    '#type' => 'fieldset',
+    '#title' => t('Step 2: Storage'),
+    '#description' => '',
+    '#collapsible' => TRUE,
+    '#collapsed' => TRUE,
+  ];
+  $form['store_summary']['details'] = [
+    '#type' => 'item',
+    '#title' => t('Storage backend'),
+    '#markup' => $stores[$default_store]['label']
+  ];
+  $form['term_summary']['step1-return'] = array(
+    '#type' => 'submit',
+    '#value' => t('Pick a different term'),
+    '#name' => 'step1-return',
+  );  
+}
 
-  return $form;
+/**
+ * Builds step1 of the tripal_admin_add_type_form()
+ */
+function tripal_admin_add_type_form_step3(&$form, &$form_state, $stores) {
+  $default_store = $form_state['values']['store_select'];
+  
+  $selected_store_module = $stores[$default_store]['module'];
+  
+  $function = $selected_store_module . '_field_storage_bundle_mapping_form';
+  if (function_exists($function)) {
+    $store_form = $function($form, $form_state, $selected_term, $submit_disabled);
+    $form['storage'][$store_type] = $store_form;
+  }
+  
+  // Add in the button for the cases of no terms or too many.
+  $form['submit_button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Create content type'),
+    '#name' => 'use_cvterm',
+    '#disabled' => $submit_disabled,
+  );
 }
 /**
  * Implements an AJAX callback for the tripal_chado_vocab_select_term_form.
@@ -755,10 +763,31 @@ function tripal_admin_add_type_form_ajax_callback($form, $form_state) {
 function tripal_admin_add_type_form_validate($form, &$form_state) {
   $stores = module_invoke_all('vocab_storage_info');
   $store_select = (isset($form_state['values']['store_select'])) ? $form_state['values']['store_select'] : NULL;
+  $clicked_button = $form_state['clicked_button']['#name'];
 
-  if (array_key_exists('clicked_button', $form_state) and
-      $form_state['clicked_button']['#name'] =='use_cvterm') {
-
+  if ($clicked_button =='step1-continue') {
+    $form_state['rebuild'] = TRUE;
+    $form_state['stage'] = 'step2';   
+    
+    $selected = tripal_get_term_lookup_form_result($form, $form_state);
+    if (count($selected) == 0) {
+      form_set_error('term_match][term_name', 'Please select a vocabulary term.');
+    }
+    if (count($selected) > 1) {
+      form_set_error('term_match][term_name', 'Please select only one vocabulary term.');
+    }
+    
+  }
+  if ($clicked_button =='step1-return') {
+    $form_state['rebuild'] = TRUE;
+    $form_state['stage'] = 'step1';
+  }
+  if ($clicked_button =='step2-continue') {
+    $form_state['rebuild'] = TRUE;
+    $form_state['stage'] = 'step3';
+  }
+  
+  if ($clicked_button =='use_cvterm') {       
     $cvterm_id = NULL;
 
     // Make sure we have a cvterm selected
@@ -797,8 +826,6 @@ function tripal_admin_add_type_form_validate($form, &$form_state) {
       }
     }
   }
-  // For any other button click it's an AJAX call and we just want to reubild
-  // the form.
   else {
     $form_state['rebuild'] = TRUE;
   }

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -845,10 +845,6 @@ function tripal_chado_field_storage_bundle_mapping_form($form, &$form_state,
       and $form_state['values']['type_column']) {
     $default['type_column'] = $form_state['values']['type_column'];
   }
-  if (array_key_exists('type_column_ignore', $form_state['values'])
-    and $form_state['values']['type_column_ignore']) {
-      $default['type_column_ignore'] = $form_state['values']['type_column_ignore'];
-  } 
   if (array_key_exists('prop_term_name', $form_state['values'])
       and $form_state['values']['prop_term_name']) {
     $default['prop_term_name'] = $form_state['values']['prop_term_name'];
@@ -865,6 +861,8 @@ function tripal_chado_field_storage_bundle_mapping_form($form, &$form_state,
       and $form_state['values']['chado_type_cv_id']) {
     $default['cv_id'] = $form_state['values']['chado_type_cv_id'];
   }
+  
+  dpm($default);
 
   $form['selected_cvterm_id'] = array(
     '#type' => 'value',
@@ -929,17 +927,11 @@ function tripal_chado_field_storage_bundle_mapping_form($form, &$form_state,
 
   // If the type_column is set then we're done!  We know the deafult table
   // and column to map this data type.
-  if (!empty($default['type_column'])) {
+  if (!empty($default['type_column']) and $default['type_column'] != 'none') {
     $submit_disabled = FALSE;
     return $form;
   }
-  
-  // If the type column is not disabled and the user has not selected
-  // a type then return.
-  if (!$default['type_column_ignore'] and empty($default['type_column'])) {
-    return $form;
-  }
-    
+     
   // Let's set the names of the linker and prop table for use below.
   $linker_table = $default['table'] . '_cvterm';
   $prop_table = $default['table']. 'prop';
@@ -1025,7 +1017,7 @@ function tripal_chado_field_storage_bundle_mapping_form_add_type(&$form,
     '#description' => 'Please select the column in the "' .
       $default['table'] . '" table that will identify a record as being of type "' .
       $term_name . '". If you select "--None--" then you will be asked
-      if you the type can be identified using a property or linker table.
+      if the type can be identified using a property or linker table.
       Only fields that have a foreign key to the cvterm table will be listed.',
     '#default_value' => $default_column,
     '#ajax' => array(
@@ -1036,17 +1028,6 @@ function tripal_chado_field_storage_bundle_mapping_form_add_type(&$form,
     ),
     '#disabled' => $default_column_ignore,
   );
-  $form['type_column_ignore'] = array(
-    '#type' => 'checkbox',
-    '#title' => 'The type column does not distinguish the type',
-    '#default_value' => $default_column_ignore,
-    '#ajax' => array(
-      'callback' => "tripal_admin_add_type_form_ajax_callback",
-      'wrapper' => "tripal-vocab-select-form",
-      'effect' => 'fade',
-      'method' => 'replace'
-    ),
-  );
 
   // Set the default value so we can short circuit the form.
   $default['type_column'] = $default_column;
@@ -1140,90 +1121,61 @@ function tripal_chado_field_storage_bundle_mapping_form_add_prop(&$form,
   );
 
   if ($default['use_prop'] == 'Yes') {
+    
     $prop_term_name = $default['prop_term_name'];
     $prop_term_value = $default['prop_term_value'];
-
-    $form['prop_term_name'] = array(
-      '#title'       => t('Property Type'),
-      '#type'        => 'textfield',
-      '#description' => t('The content type "' . $term->name . '" must be
+    
+    // We need a term lookup form for the property type.
+    $description = t('The content type "' . $term->name . '" must be
           associated with a property type.  The property type must be the
           name of a term in a controlled vocabulary and the controlled
           vocabulary should already be loaded into Tripal. Please select
           the property type that will be used to identify records of this
-          type'),
-      '#required'    => TRUE,
-      '#default_value' => $prop_term_name,
-      '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/",
-    );
-    $form['prop_term_select_button'] = array(
-      '#type' => 'submit',
-      '#value' => t('Lookup Term'),
-      '#name' => 'select_prop_cvterm',
-      '#ajax' => array(
-        'callback' => "tripal_admin_add_type_form_ajax_callback",
-        'wrapper' => "tripal-vocab-select-form",
-        'effect' => 'fade',
-        'method' => 'replace'
-      ),
-    );
-    // If the term has been provided by the user then we want to search for
-    // matching terms in the database and let them select among any matches.
-    if ($prop_term_name) {
-      $form['prop_terms_list'] = array(
-        '#type' => 'fieldset',
-        '#title' => t('Matching Terms'),
-        '#description' => t('Please select the term the best matches the
-          property type.')
-      );
-      $match = array(
-        'name' => $prop_term_name,
-      );
-      $pterms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));
-      $pterms = chado_expand_var($pterms, 'field', 'cvterm.definition');
-      $num_terms = 0;
-
-      // Let the user select from any matching terms. Sometimes there may be
-      // more than one that match.
-      foreach ($pterms as $pterm) {
-        // Save the user a click by setting the default value as 1 if there's
-        // only one matching term.
-        $default = FALSE;
-        $attrs = array();
-        if ($num_terms == 0 and count($pterms) == 1) {
-          $default = TRUE;
-          $attrs = array('checked' => 'checked');
+          type');
+    tripal_get_term_lookup_form($form, $form_state, $prop_term_name,
+      'Property Type', $description, TRUE, '', 1,
+      'tripal_admin_add_type_form_ajax_callback');
+    
+    // If a base table has a 'type_id' field then we must have the user
+    // specify the base table type as well.
+    $base_type_column = FALSE;
+    $schema = chado_get_schema($default['table']);
+    foreach ($schema['foreign keys'] as $fk_id => $details) { 
+      if ($details['table'] == 'cvterm') {
+        foreach ($details['columns'] as $fk_left => $fk_right) {
+          if ($fk_left == 'type_id') {
+            $base_type_column = 'type_id';
+          }
         }
-        $term_element_name = 'prop_term-' . $pterm->cvterm_id;
-        $form['prop_terms_list'][$term_element_name] = array(
-          '#type' => 'checkbox',
-          '#title' =>  $pterm->name,
-          '#default_value' => $default,
-          '#attributes' => $attrs,
-          '#description' => '<b>Vocabulary:</b> ' . $pterm->cv_id->name . ' (' . $pterm->dbxref_id->db_id->name . ') ' . $pterm->cv_id->definition .
-            '<br><b>Term: </b> ' . $pterm->dbxref_id->db_id->name . ':' . $pterm->dbxref_id->accession . '.  ' .
-            '<br><b>Definition:</b>  ' . $pterm->definition,
-          '#ajax' => array(
-            'callback' => "tripal_admin_add_type_form_ajax_callback",
-            'wrapper' => "tripal-vocab-select-form",
-            'effect' => 'fade',
-            'method' => 'replace'
-          ),
-        );
-        $num_terms++;
       }
-
-      $form['prop_term_value'] = array(
-        '#type' => 'textfield',
-        '#title' => 'Property Value',
-        '#description' => t('All properties have a type and a value.  Above you
-            indicated the type of property. Now you must specify the value
-            that this properly must have in order to be considered of
-            type "' . $term->name . '".'),
-        '#default_value' => $prop_term_value,
-        '#required' => TRUE,
-      );
     }
+    
+    if ($base_type_column) {
+      $description = t('The ' . $default['table'] . ' table of Chado requires 
+        that each record have a type.  You have indicated that this
+        content type is not distinguished by a column in the base tabe but
+        instead by a property.  However, the ' . $default['table'] . ' requires 
+        that a value be given for the ' . $base_type_column . '. Please indicate 
+        what this type should be.  For example.  If you are storing genetic 
+        markers in the feature table and you want to refer to all markers as
+        genetic markers but you specify the type of marker in the featureprop table
+        then here you would enter the term for the genetic marker and in the
+        Property Type you would indicate the term for the marker type.');
+      tripal_get_term_lookup_form($form, $form_state, $prop_term_name,
+        'Base Type', $description, TRUE, '', 1,
+        'tripal_admin_add_type_form_ajax_callback');
+    }
+
+    $form['prop_term_value'] = array(
+      '#type' => 'textfield',
+      '#title' => 'Property Value',
+      '#description' => t('All properties have a type and a value.  Above you
+          indicated the type of property. Now you must specify the value
+          that this properly must have in order to be considered of
+          type "' . $term->name . '".'),
+      '#default_value' => $prop_term_value,
+      '#required' => TRUE,
+    );
   }
 }
 

tripal_chado/includes/tripal_chado.vocab_storage.inc

@@ -368,4 +368,4 @@ function tripal_chado_vocab_import_form_validate($form, &$form_state) {
 function tripal_chado_vocab_import_form_submit($form, &$form_state) {
   module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.obo_loader');
   return tripal_cv_obo_form_submit($form, $form_state);
-}
+}