Added new chado_bundle table to link a bundle directly to a chado table. Previously it was mapped via the chado_cvterm_mapping table which mapped cvterms but wasn't exact enough for bundles. Also improved the content creation form to allow for more customization for how bundles are mapped to Chado

tripal/api/tripal.entities.api.inc

@@ -165,11 +165,13 @@ function tripal_load_bundle_entity($values) {
  *
  * @param $bundle
  *   The newly created TripalBundle object.
- * @param $args
- *   Arguments used to create the TripalBundle, as well as
- *   arugments from the form submission.
+ * @param $storage_args
+ *   Arguments passed to the storage backend for this bundle.  These arguments
+ *   typically provide details for how to associate this bundle with records
+ *   in the storage system.  Each storage system will have its own set of
+ *   arguments that it will expect.
  */
-function hook_bundle_create(&$bundle, $args) {
+function hook_bundle_create(&$bundle, $storage_args) {
 
 }
 /**
@@ -188,12 +190,13 @@ function hook_bundle_create(&$bundle, $args) {
  *  A string, passed by reference, that is filled with the error message
  *  if the function fails.
  * @return
- *  TRUE if the entity type (bundle) was succesfully created.  FALSE otherwise.
+ *   The bundle object or FALSE if failure.
  */
 function tripal_create_bundle($args, &$error = '') {
   $vocabulary = $args['vocabulary'];
   $accession = $args['accession'];
   $term_name = $args['term_name'];
+  $storage_args = $args['storage_args'];
 
   $transaction = db_transaction();
   try {
@@ -235,7 +238,7 @@ function tripal_create_bundle($args, &$error = '') {
     $modules = module_implements('bundle_create');
     foreach ($modules as $module) {
       $function = $module . '_bundle_create';
-      $function($bundle, $args);
+      $function($bundle, $storage_args);
     }
 
     // Clear the entity cache so that Drupal will read our
@@ -257,7 +260,7 @@ function tripal_create_bundle($args, &$error = '') {
     return FALSE;
   }
 
-  return TRUE;
+  return $bundle;
 }
 
 /**
@@ -486,19 +489,19 @@ function tripal_set_bundle_variable($variable_name, $bundle_id, $value) {
 /**
  * Get Page Title Format for a given Tripal Entity Type.
  *
- * @param TripalBundle $entity
+ * @param TripalBundle $bundle
  *   The Entity object for the Tripal Bundle the title format is for.
  */
-function tripal_get_title_format($entity) {
+function tripal_get_title_format($bundle) {
 
   // Get the existing title format if it exists.
-  $title_format = tripal_get_bundle_variable('title_format', $entity->id);
+  $title_format = tripal_get_bundle_variable('title_format', $bundle->id);
 
   // If there isn't yet a title format for this bundle/type then we should
   // determine the default.
   if (!$title_format) {
-    $title_format = tripal_get_default_title_format($entity);
-    tripal_save_title_format($entity, $title_format);
+    $title_format = tripal_get_default_title_format($bundle);
+    tripal_save_title_format($bundle, $title_format);
   }
 
   return $title_format;
@@ -520,22 +523,22 @@ function tripal_save_title_format($entity, $format) {
 /**
  * Determine the default title format to use for an entity.
  *
- * @param TripalBundle $entity
+ * @param TripalBundle $bundle
  *   The Entity object for the Tripal Bundle that the title format is for.
  *
  * @return string
  *   A default title format.
  */
-function tripal_get_default_title_format($entity) {
+function tripal_get_default_title_format($bundle) {
   $format = '';
 
   // Retrieve all available tokens.
-  $tokens = tripal_get_entity_tokens($entity);
+  $tokens = tripal_get_entity_tokens($bundle);
 
   // A) Check to see if more informed modules have suggested a title for this
   //    type. Invoke hook_tripal_default_title_format() to get all suggestions
   //    from other modules.
-  $suggestions = module_invoke_all('tripal_default_title_format', $entity, $tokens);
+  $suggestions = module_invoke_all('tripal_default_title_format', $bundle, $tokens);
   if ($suggestions) {
     // Use the suggestion with the lightest weight.
     $lightest_key = NULL;
@@ -547,15 +550,7 @@ function tripal_get_default_title_format($entity) {
     return $format;
   }
 
-  // B) Check to see if any fields contain "name" in the machine name and if
-  //    so, use them.
-  $name_fields = preg_grep('/name/', array_keys($tokens));
-  if ($name_fields AND !$format) {
-    $format = implode(', ', $name_fields);
-    return $format;
-  }
-
-  // C) Generate our own ugly title by simply comma-separating all the
+  // B) Generate our own ugly title by simply comma-separating all the
   //    required fields.
   if (!$format) {
     $tmp = array();
@@ -576,7 +571,7 @@ function tripal_get_default_title_format($entity) {
 /**
  * Implement this hook to define default formats for Tripal Content Types.
  *
- * @param TripalBundle $entity
+ * @param TripalBundle $bundle
  *   A tripal content type entity with information to be used for determining the default title format.
  * @param array $available_tokens
  *   An array of available tokens for this particular tripal content type.
@@ -593,13 +588,13 @@ function tripal_get_default_title_format($entity) {
  *    - format: a string including approved tokens used to determine the title
  *        on Tripal content pages.
  */
-function hook_tripal_default_title_format($entity, $available_tokens) {
+function hook_tripal_default_title_format($bundle, $available_tokens) {
   $format = array();
 
   // If you want to suggest a default format for a particular vocabulary term:
   //---------------------------------------------------------------------------
   // Load the term associated with this Tripal Content type.
-  $term = entity_load('TripalTerm', array('id' => $entity->term_id));
+  $term = entity_load('TripalTerm', array('id' => $bundle->term_id));
   $term = reset($term);
 
   // If it's the term you are interested in then suggest a format.

tripal/api/tripal.terms.api.inc

@@ -29,7 +29,7 @@
 function hook_vocab_storage_info() {
   return array(
     'term_chado_storage' => array(
-      'label' => t('Chado storage'),
+      'label' => t('Chado'),
       'description' => t('Integrates terms stored in the local Chado database with Tripal entities.'),
       'settings' => array(),
     ),

tripal/includes/TripalBundleController.inc

@@ -45,19 +45,19 @@ class TripalBundleController extends EntityAPIControllerExportable {
    * @param DatabaseTransaction $transaction
    */
   public function delete($ids, DatabaseTransaction $transaction = NULL) {
-    $entities = $ids ? $this->load($ids) : FALSE;
+    $bundles = $ids ? $this->load($ids) : FALSE;
 
     if (!$transaction) {
       $transaction = db_transaction();
     }
 
-    if ($entities) {
+    if ($bundles) {
 
-      foreach ($entities as $id => $entity) {
+      foreach ($bundles as $id => $bundle) {
 
         // Find any TripalEntity fields that are attached to this bundle and
         // remove them.
-        $instances = field_info_instances('TripalEntity', $entity->name);
+        $instances = field_info_instances('TripalEntity', $bundle->name);
         foreach ($instances as $instance) {
           // Mark the instance as deleted and purge it.
           $field = field_info_field($instance['field_name']);
@@ -67,18 +67,18 @@ class TripalBundleController extends EntityAPIControllerExportable {
           // If the field has no more instances then purge it too.
           if (count($field['bundles']) == 1 and
               count($field['bundles']['TripalEntity']) == 1 and
-              in_array($entity->name, $field['bundles']['TripalEntity'])) {
+              in_array($bundle->name, $field['bundles']['TripalEntity'])) {
             field_purge_field($field);
           }
         }
 
         // TODO: this Chado sepcific code needs to be moved out of here!
 
-        // Remove the entries in the chado_entity and tripal_entity t
+        // Remove the entries in the chado_entity and tripal_entity
         $query = db_select('chado_entity', 'ce');
         $query->join('tripal_entity', 'te', 'te.id = ce.entity_id');
         $records = $query->fields('ce', array('chado_entity_id', 'data_table', 'record_id'))
-          ->condition('te.bundle', $entity->name)
+          ->condition('te.bundle', $bundle->name)
           ->execute();
         $num_removed = 0;
         while ($record = $records->fetchObject()) {
@@ -90,13 +90,16 @@ class TripalBundleController extends EntityAPIControllerExportable {
             ->execute();
           $num_removed++;
         }
+        db_delete('chado_bundle')
+          ->condition('bundle_id', $bundle->id)
+          ->execute();
         if ($num_removed > 0) {
           drupal_set_message(t('Removed %num records', array('%num' => $num_removed)));
         }
 
         // Remove the terms for the bundles that are to be deleted.
         db_delete('tripal_term')
-          ->condition('id', $entity->term_id)
+          ->condition('id', $bundle->term_id)
           ->execute();
       }
 
@@ -106,8 +109,8 @@ class TripalBundleController extends EntityAPIControllerExportable {
       // Not sure what this does, but copied from the
       // EntityAPIControllerExportable->delete() function which this one
       // overrides.
-      foreach ($entities as $id => $entity) {
-        if (entity_has_status($this->entityType, $entity, ENTITY_IN_CODE)) {
+      foreach ($bundles as $id => $bundle) {
+        if (entity_has_status($this->entityType, $bundle, ENTITY_IN_CODE)) {
           entity_defaults_rebuild(array($this->entityType));
           break;
         }

tripal/includes/TripalBundleUIController.inc

@@ -33,8 +33,6 @@ class TripalBundleUIController extends EntityDefaultUIController {
       'page callback' => 'drupal_get_form',
       'page arguments' => array('tripal_admin_add_type_form'),
       'access arguments' => array('administer tripal data types'),
-      'file' =>  'includes/tripal.admin.inc',
-      'file path' => drupal_get_path('module', 'tripal'),
       'type' => MENU_LOCAL_ACTION,
       'weight' => 2
     );
@@ -406,24 +404,429 @@ function tripal_bundle_access($op, $type = NULL, $account = NULL) {
  */
 function tripal_admin_add_type_form($form, &$form_state) {
 
-  // TODO: we need some sort of administrative interface that lets the user
-  // switch to the desired vocabulary type. For now, we'll just use the
-  // first one in the list.
+  // TODO: the Chado specific function calls should not be here.  They need
+  // to be genericized.
   $stores = module_invoke_all('vocab_storage_info');
-  if (is_array($stores) and count($stores) > 0) {
-    $keys = array_keys($stores);
-    $module = $stores[$keys[0]]['module'];
-    $function = $module . '_vocab_select_term_form';
-    if (function_exists($function)) {
-      $form = $function($form, $form_state);
-    }
-  }
-  else {
+  if (!is_array($stores) or count($stores) == 0) {
     tripal_set_message('A storage backend is not enabled for managing
           the vocabulary terms used to create content.  Please enable
           a module that supports storage of vocabualary terms (e.g. tripal_chado)
           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);
+  }
+
+  $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
+
+  // 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
+        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/",
+  );
+  $form['select_button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Lookup Term'),
+    '#name' => 'select_cvterm',
+    '#ajax' => array(
+      'callback' => "tripal_admin_add_type_form_ajax_callback",
+      'wrapper' => "tripal-vocab-select-form",
+      'effect' => 'fade',
+      'method' => 'replace'
+    ),
+  );
+
+  if ($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;
+    $selected_term_id = '';
+    foreach ($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_id = $term->cvterm_id;
+      }
+      $num_terms++;
+    }
+    if ($num_terms == 0) {
+      $form['terms_list']['none'] = array(
+        '#type' => 'item',
+        '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
+      );
+    }
+    $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: we should have a default store setting so that user's have
+    // fewer clicks.
+
+    // 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 sotrage 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) {
+      if ($store_type == 'term_chado_storage') {
+        // TODO: Move this Chado-specific code out of there.
+        $default_table = '';
+        if (array_key_exists('base_chado_table', $form_state['values'])
+            and $form_state['values']['base_chado_table']) {
+          $default_table = $form_state['values']['base_chado_table'];
+        }
+        else {
+          $mapped_table = chado_get_cvterm_mapping(array('cvterm_id' => $selected_term_id));
+          if ($mapped_table) {
+            $default_table = $mapped_table->chado_table;
+          }
+        }
+
+        $form['storage'][$store_type]['selected_cvterm_id'] = array(
+          '#type' => 'value',
+          '#value' => $selected_term_id,
+        );
+
+        $base_tables = chado_get_base_tables();
+        $options = array(0 => '-- Select table --');
+        foreach ($base_tables AS $tablename) {
+          $options[$tablename] = $tablename;
+        }
+        $form['storage'][$store_type]['base_chado_table'] = array(
+          '#type' => 'select',
+          '#title' => 'Chado table',
+          '#options' => $options,
+          '#description' => 'Select the Chado table into which the primary records for this content type will be stored.',
+          '#default_value' => $default_table,
+          '#ajax' => array(
+            'callback' => "tripal_admin_add_type_form_ajax_callback",
+            'wrapper' => "tripal-vocab-select-form",
+            'effect' => 'fade',
+            'method' => 'replace'
+          ),
+        );
+        $form_state['input']['base_chado_table'] = $default_table;
+
+        if ($default_table) {
+
+          // There are a few places in form below where the type columns
+          // can be used to identify a record. So, we'll create the
+          // select options here so it can be used multiple places.  We
+          // only want to include in our column options those fields that
+          // are foreign keys to the cvterm table
+          $schema = chado_get_schema($default_table);
+          $column_options = array('0' => '--Select column--');
+          $cvt_fkeys = array_keys($schema['foreign keys']['cvterm']['columns']);
+          foreach ($schema['fields'] as $column_name => $column_details) {
+            if (in_array($column_name, $cvt_fkeys)) {
+              $column_options[$column_name] = $column_name;
+            }
+          }
+
+          $default_has_all = 'No';
+          if (array_key_exists('chado_table_has_all', $form_state['values'])
+              and $form_state['values']['chado_table_has_all']) {
+            $default_has_all = $form_state['values']['chado_table_has_all'];
+          }
+          $form['storage'][$store_type]['chado_table_has_all'] = array(
+            '#type' => 'radios',
+            '#options' => array(
+              'Yes' => 'Yes',
+              'No' => 'No'
+            ),
+            '#title' => 'Are all records in the "' . $default_table .
+              '" table of type "'. $term_name . '"?',
+            '#description' => 'Select "Yes" if the "' .
+              $default_table . '" table houses more that just data of type "' .
+              $term_name . '".',
+            '#default_value' => $default_has_all,
+            '#ajax' => array(
+              'callback' => "tripal_admin_add_type_form_ajax_callback",
+              'wrapper' => "tripal-vocab-select-form",
+              'effect' => 'fade',
+              'method' => 'replace'
+            ),
+          );
+
+          // If the table does not contain just one single type of record.
+          if ($default_has_all == 'No') {
+
+            $default_type_column = '';
+            if (array_key_exists('type_id', $schema['fields'])) {
+              $default_type_column = 'type_id';
+            }
+
+            // If the table doesn't have an obvious type_id column then
+            // let the user specify how record types are identified.
+            if ($default_type_column) {
+
+              $default_has_type = 'Yes';
+              if (array_key_exists('chado_table_has_type', $form_state['values'])
+                  and $form_state['values']['chado_table_has_type']) {
+                $default_has_type = $form_state['values']['chado_table_has_type'];
+              }
+              $form['storage'][$store_type]['chado_table_has_type'] = array(
+                '#type' => 'radios',
+                '#title' => 'Do you want to use the "' . $default_table . '.' .
+                   $default_type_column . '" to distinguish between content types?',
+                '#options' => array(
+                  'Yes' => 'Yes',
+                  'No' => 'No'
+                ),
+                '#description' => t('Many tables in Chado use a "type_id" column
+                    to identify specific data types. For example, the "feature.type_id"
+                    column is used to distinguish between different types of
+                    genomic features that are all housed in the feature table.
+                    But there is sometimes a cvterm linker table where additional
+                    attributes for the record can be set.  Here you can specify if you
+                    want to use the type_id column or select another way
+                    to identify records in the "' . $default_table . '" table that
+                    are of this type'),
+                '#default_value' => $default_has_type,
+                '#ajax' => array(
+                  'callback' => "tripal_admin_add_type_form_ajax_callback",
+                  'wrapper' => "tripal-vocab-select-form",
+                  'effect' => 'fade',
+                  'method' => 'replace'
+                ),
+              );
+
+              // If the type_id column is not wanted to differentiate between
+              // different records of this type then find out if the user wants
+              // to use a linker cvterm table, but only if one exists
+              $linker_table = $default_table . '_cvterm';
+              if ($default_has_type == "Yes") {
+                $submit_disabled = FALSE;
+              }
+              else if ($default_has_type == 'No' and chado_table_exists($linker_table)) {
+                $default_use_linker = 'Yes';
+                if (array_key_exists('chado_type_use_linker', $form_state['values'])
+                    and $form_state['values']['chado_type_use_linker']) {
+                  $default_use_linker = $form_state['values']['chado_type_use_linker'];
+                }
+                $form['storage'][$store_type]['chado_type_use_linker'] = array(
+                  '#type' => 'radios',
+                  '#title' => 'Do you want to use the "' . $linker_table . '" table
+                     to distinguish between content types?',
+                  '#options' => array(
+                    'Yes' => 'Yes',
+                    'No' => 'No'
+                  ),
+                  '#description' => t('Sometimes records can be distringuish
+                      using a linker table, especially if there is no column
+                      in the specified Chado table to identify the
+                      record types. In these cases the linker table is
+                      sometimes used.'),
+                  '#default_value' => $default_use_linker,
+                  '#ajax' => array(
+                    'callback' => "tripal_admin_add_type_form_ajax_callback",
+                    'wrapper' => "tripal-vocab-select-form",
+                    'effect' => 'fade',
+                    'method' => 'replace'
+                  ),
+                );
+
+                if($default_use_linker == 'No') {
+                  if (count(array_keys($column_options)) == 1) {
+                    $form['storage'][$store_type]['type_column'] = array(
+                      '#type' => 'item',
+                      '#title' => 'Type Column',
+                      '#description' => 'The  "' . $default_table .
+                        '" table does not have a column
+                        that stores data types. You cannot map the "' .
+                        $term_name . '" type to this table.',
+                    );
+                  }
+                  else {
+                    $form['storage'][$store_type]['type_column'] = array(
+                      '#type' => 'select',
+                      '#title' => 'Type Column',
+                      '#options' => $column_options,
+                      '#description' => 'Please select the column in the "' .
+                        $default_table . '" table that will identify a record
+                        as being of type "' . $term_name . '".',
+                      '#default_value' => $default_type_column,
+                      '#ajax' => array(
+                        'callback' => "tripal_admin_add_type_form_ajax_callback",
+                        'wrapper' => "tripal-vocab-select-form",
+                        'effect' => 'fade',
+                        'method' => 'replace'
+                      ),
+                    );
+                    $submit_disabled = FALSE;
+                  }
+                } // end if(!$default_use_linker) {
+                else {
+                  $submit_disabled = FALSE;
+                }
+              } // end if ($default_has_type == 'No' and ...
+            } // end else if ($default_type_column) {
+            else {
+              // If the type_id column is not wanted to differentiate between
+              // different records of this type then find out if the user wants
+              // to use a linker table, but only if one exists
+              $linker_table = $default_table . '_cvterm';
+              if (chado_table_exists($linker_table)) {
+                $default_use_linker = 'Yes';
+                if (array_key_exists('chado_type_use_linker', $form_state['values'])
+                    and $form_state['values']['chado_type_use_linker']) {
+                  $default_use_linker = $form_state['values']['chado_type_use_linker'];
+                }
+                $form['storage'][$store_type]['chado_type_use_linker'] = array(
+                  '#type' => 'radios',
+                  '#title' => 'Do you want to use the "' . $linker_table . '" table
+                     to distinguish between content types?',
+                  '#options' => array(
+                    'Yes' => 'Yes',
+                    'No' => 'No'
+                  ),
+                  '#description' => t('Sometimes records can be distringuish
+                      using a linker, especially if there is no column
+                      in the specified Chado table to identify the
+                      record types. In these cases the linker table is
+                      sometimes used.'),
+                  '#default_value' => $default_use_linker,
+                  '#ajax' => array(
+                    'callback' => "tripal_admin_add_type_form_ajax_callback",
+                    'wrapper' => "tripal-vocab-select-form",
+                    'effect' => 'fade',
+                    'method' => 'replace'
+                  ),
+                );
+
+                if($default_use_linker == 'No') {
+                  if (count(array_keys($column_options)) == 1) {
+                    $form['storage'][$store_type]['type_column'] = array(
+                      '#type' => 'item',
+                      '#title' => 'Type Column',
+                      '#description' => 'The  "' . $default_table .
+                        '" table does not have a column
+                        that stores data types. You cannot map the "' .
+                        $term_name . '" type to this table.',
+                    );
+                  }
+                  else {
+                    $form['storage'][$store_type]['type_column'] = array(
+                      '#type' => 'select',
+                      '#title' => 'Type Column',
+                      '#options' => $column_options,
+                      '#description' => 'Please select the column in the "' .
+                        $default_table . '" table that will identify a record
+                        as being of type "' . $term_name . '".',
+                      '#default_value' => $default_type_column,
+                      '#ajax' => array(
+                        'callback' => "tripal_admin_add_type_form_ajax_callback",
+                        'wrapper' => "tripal-vocab-select-form",
+                        'effect' => 'fade',
+                        'method' => 'replace'
+                      ),
+                    );
+                    $submit_disabled = FALSE;
+                  }
+                } // end if(!$default_use_linker) {
+                else {
+                  $submit_disabled = FALSE;
+                }
+              } // end if ($default_has_type == 'No' and ...
+            } // end else
+          } //  end if ($default_has_all == 'No') {
+          else {
+            $submit_disabled = FALSE;
+          }
+        } // end if ($default_table) {
+      } // end if ($default_store) {
+      // 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,
+      );
+    }
   }
+
+  $form['#prefix'] = '<div id = "tripal-vocab-select-form">';
+  $form['#suffix'] = '</div>';
+
+
+  return $form;
+}
+/**
+ * Implements an AJAX callback for the tripal_chado_vocab_select_term_form.
+ */
+function tripal_admin_add_type_form_ajax_callback($form, $form_state) {
   return $form;
 }
 /**
@@ -431,47 +834,101 @@ function tripal_admin_add_type_form($form, &$form_state) {
  *
  */
 function tripal_admin_add_type_form_validate($form, &$form_state) {
-  // TODO: we need some sort of administrative interface that lets the user
-  // switch to the desired vocabulary type. For now, we'll just use the
-  // first one in the list.
   $stores = module_invoke_all('vocab_storage_info');
-  if (is_array($stores) and count($stores) > 0) {
-    $keys = array_keys($stores);
-    $module = $stores[$keys[0]]['module'];
-    $function = $module . '_vocab_select_term_form_validate';
-    if (function_exists($function)) {
-      $function($form, $form_state);
+  $keys = array_keys($stores);
+  $module = $stores[$keys[0]]['module'];
+  $function = $module . '_vocab_select_term_form_validate';
+  if (function_exists($function)) {
+    $function($form, $form_state);
+  }
+
+  if (array_key_exists('clicked_button', $form_state) and
+      $form_state['clicked_button']['#name'] =='use_cvterm') {
+
+    $cvterm_id = NULL;
+
+    // Make sure we have a cvterm selected
+    $num_selected = 0;
+    foreach ($form_state['values'] as $key => $value) {
+      $matches = array();
+      if (preg_match("/^term-(\d+)$/", $key, $matches) and
+          $form_state['values']['term-' . $matches[1]]) {
+        $cvterm_id = $matches[1];
+        $term = chado_generate_var('cvterm', array('cvterm_id' => $cvterm_id));
+        $num_selected++;
+      }
+    }
+    if ($num_selected == 0) {
+      form_set_error('', 'Please select at least one term.');
+    }
+    else if ($num_selected > 1) {
+      form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
     }
+    else {
+      $form_state['term']['vocabulary'] = $term->dbxref_id->db_id->name;
+      $form_state['term']['accession'] = $term->dbxref_id->accession;
+      $form_state['term']['term_name'] = $term->name;
+
+      // Make sure a default table is selected
+      // TODO: move this Chado specific code out.
+      $default_table = $form_state['values']['base_chado_table'];
+      if (!$default_table) {
+        form_set_error('base_chado_table', 'Please select a default table.');
+      }
+    }
+  }
+  // For any other button click it's an AJAX call and we just want to reubild
+  // the form.
+  else {
+    $form_state['rebuild'] = TRUE;
   }
 }
 /**
  * Implements hook_submit() for the tripal_admin_add_type_form.
- *
- * The storage backend must set the
- *
  */
 function tripal_admin_add_type_form_submit($form, &$form_state) {
   $vocabulary = '';
   $accession = '';
-  if (array_key_exists('storage', $form_state)) {
-    $storage = $form_state['storage'];
-    $vocabulary = array_key_exists('vocabulary', $storage) ? $storage['vocabulary'] : '';
-    $accession = array_key_exists('accession', $storage) ? $storage['accession'] : '';
-    $term_name = array_key_exists('term_name', $storage) ? $storage['term_name'] : '';
+  if (array_key_exists('term', $form_state)) {
+    $selected_term = $form_state['term'];
+    $vocabulary = array_key_exists('vocabulary', $selected_term) ? $selected_term['vocabulary'] : '';
+    $accession = array_key_exists('accession', $selected_term) ? $selected_term['accession'] : '';
+    $term_name = array_key_exists('term_name', $selected_term) ? $selected_term['term_name'] : '';
 
     // Before we try to add this type, check to see if it already exists
     // as a bundle.
     $term = tripal_load_term_entity(array('vocabulary' => $vocabulary, 'accession' => $accession));
     if (!$term) {
       $error = '';
+      // TODO: the storage args are Chado specific. This should be made
+      // more generic to support other back-ends.
+      $storage_args = array();
+      if (array_key_exists('base_chado_table', $form_state['values'])) {
+        $storage_args['data_table'] = $form_state['values']['base_chado_table'];
+      }
+      if (array_key_exists('chado_type_use_linker', $form_state['values']) and
+          $form_state['values']['chado_type_use_linker'] == 'Yes') {
+        $storage_args['type_linker_table'] = $form_state['values']['base_chado_table'] . '_cvterm';
+        $storage_args['type_column'] = 'cvterm_id';
+      }
+      if (array_key_exists('chado_table_has_type', $form_state['values']) and
+          $form_state['values']['chado_table_has_type'] == 'Yes') {
+        $storage_args['type_column'] = 'type_id';
+      }
+      if (array_key_exists('type_column', $form_state['values']) and
+          $form_state['values']['type_column']) {
+        $storage_args['type_column'] = $form_state['values']['type_column'];
+      }
+
+      $storage_args['type_id'] = $form_state['values']['selected_cvterm_id'];
       $args = array(
         'vocabulary' => $vocabulary,
         'accession' => $accession,
         'term_name' => $term_name,
-        'form_values' => $form_state['values'],
+        'storage_args' => $storage_args,
       );
-      $success = tripal_create_bundle($args, $error);
-      if (!$success) {
+      $bundle = tripal_create_bundle($args, $error);
+      if (!$bundle) {
         drupal_set_message($error, 'error');
         $form_state['redirect'] = "admin/structure/bio_data";
       }
@@ -479,6 +936,10 @@ function tripal_admin_add_type_form_submit($form, &$form_state) {
         drupal_set_message('New data type created.');
         $form_state['redirect'] = "admin/structure/bio_data";
       }
+
+      // TODO: move these Chado specific settings out.
+
+
     }
     else {
       drupal_set_message("The term '$accession' already exists as a content type.", 'warning');

tripal/tripal.module

@@ -576,4 +576,4 @@ function tripal_form_alter(&$form, $form_state, $form_id) {
   if ($form_id == 'field_ui_field_edit_form' and $form['#instance']['entity_type'] == 'TripalEntity') {
     tripal_field_instance_settings_form_alter($form, $form_state);
   }
-}
+}

tripal_chado/api/modules/tripal_chado.cv.api.inc

@@ -147,6 +147,8 @@ function tripal_get_cv_select_options() {
  *   An array apropriate for use with the chado_generate_var for uniquely
  *   identifying a cvterm record. Alternativley, there are also some specially
  *   handled keys. They are:
+ *    - id: an ID for the term of the for [dbname]:[accession], where [dbname]
+ *      is the short name of the vocabulary and accession is the unique ID.
  *    - cv_id:  an integer indicating the cv_id or an array with 'name' => the
  *      name of the cv.
  *    - synonym: an array with 'name' => the name of the synonym of the cvterm
@@ -234,6 +236,17 @@ function tripal_get_cvterm($identifiers, $options = array()) {
       $options
     );
   }
+  if (isset($identifiers['id'])) {
+    list($db_name, $accession) = preg_split('/:/', $identifiers['id']);
+    $cvterm = chado_generate_var('cvterm',array(
+      'dbxref_id' => array(
+        'db_id' => array(
+          'name' => $db_name,
+        ),
+        'accession' => $accession,
+      )
+    ));
+  }
 
   // Else we have a simple case and we can just use chado_generate_var to get the cvterm
   else {

tripal_chado/api/modules/tripal_chado.feature.api.inc

@@ -1125,7 +1125,7 @@ function chado_get_feature_relationships($feature_id, $side = 'as_subject') {
   $esql = "
     SELECT entity_id
     FROM {chado_entity}
-    WHERE data_table = 'feature' AND record_id = :feature_id";
+    WHERE record_id = :feature_id";
   $relationships = array();
   while ($rel = $results->fetchObject()) {
     $entity = db_query($esql, array(':feature_id' => $rel->subject_id))->fetchObject();

tripal_chado/api/tripal_chado.api.inc

@@ -68,51 +68,73 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
   $bundle_name = $values['bundle_name'];
   $sync_node = array_key_exists('sync_node', $values) ? $values['sync_node'] : '';
 
-
   // Load the bundle entity so we can get information about which Chado
   // table/field this entity belongs to.
   $bundle = tripal_load_bundle_entity(array('name' => $bundle_name));
-  $bundle_id = $bundle->id;
-  $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
-  $vocab = $term->vocab;
-  $params = array(
-    'vocabulary' => $vocab->vocabulary,
-    'accession' => $term->accession,
-  );
-  $mapped_table = chado_get_cvterm_mapping($params);
-  $table = $mapped_table->chado_table;
-  $column = $mapped_table->chado_field;
-  $cvterm_id = $mapped_table->cvterm->cvterm_id;
+  if (!$bundle) {
+    tripal_report_error('tripal_chado', TRIPAL_ERROR,
+        "Unknown bundle. Could not publish record: @error",
+        array('@error' => 'The bundle name must be provided'));
+    return FALSE;
+  }
+
+  $table = $bundle->data_table;
+  $type_column = $bundle->type_column;
+  $type_linker_table = $bundle->type_linker_table;
+  $cvterm_id  = $bundle->type_id;
 
   // Get the table information for the Chado table.
   $table_schema = chado_get_schema($table);
   $pkey_field = $table_schema['primary key'][0];
 
   // Construct the SQL for identifying which records should be published.
+  $args = array();
   $select = "SELECT $pkey_field as record_id ";
   $from = "
     FROM {" . $table . "} T
       LEFT JOIN public.chado_entity CE on CE.record_id = T.$pkey_field
-    AND CE.data_table = '$table'
+         AND CE.data_table = :table
   ";
 
   // For migration of Tripal v2 nodes to entities we want to include the
   // coresponding chado linker table.
   if ($sync_node && db_table_exists('chado_' . $table)) {
     $select = "SELECT T.$pkey_field as record_id, CT.nid ";
-    $from .= "INNER JOIN public.chado_$table CT ON CT.$pkey_field = T.$pkey_field";
+    $from .= " INNER JOIN public.chado_$table CT ON CT.$pkey_field = T.$pkey_field";
   }
   $where = " WHERE CE.record_id IS NULL ";
-  // TODO: here we have hard-coded the analysis and organism tables, but
-  // there may be more that don't hve a type field.  I think if the $column
-  // value is null then that check is good enough, but it needs to be looked at.
-  if ($table != 'analysis' and $table != 'organism') {
-    $where .= "AND $column = $cvterm_id";
+  $args[':table'] = $table;
+
+  // Handle bundles that use a linker property table for identifying the type
+  // of record to publish.
+  if ($type_linker_table and $type_column) {
+    $propschema = chado_get_schema($type_linker_table);
+    $fkeys = $propschema['foreign keys'][$table]['columns'];
+    foreach ($fkeys as $leftkey => $rightkey) {
+      if ($rightkey == $pkey_field) {
+        $from .= " INNER JOIN {" . $type_linker_table . "} LT ON T.$pkey_field = LT.$leftkey ";
+      }
+    }
+    $where .= "AND LT.$type_column = :cvterm_id";
+    $args[':cvterm_id'] = $cvterm_id;
+  }
+
+  // If the type column is in the base table then add in the SQL for that.
+  if (!type_linker_table and $type_column) {
+    $where .= "AND T.$type_column = :cvterm_id";
+    $args[':cvterm_id'] = $cvterm_id;
+  }
+  // If no type column is specified then we have a problem.
+  if ($type_linker_table and !$type_column) {
+    tripal_report_error('tripal_chado', TRIPAL_ERROR,
+        "Could not publish record: @error",
+        array('@error' => 'The bundle does not properly map to Chado.'));
+    return FALSE;
   }
 
   // First get the count
   $sql = "SELECT count(*) as num_records " . $from . $where;
-    $result = chado_query($sql);
+  $result = chado_query($sql, $args);
   $count = $result->fetchField();
 
   // calculate the interval for updates
@@ -123,9 +145,13 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
 
   // Perform the query.
   $sql = $select . $from . $where;
-  $records = chado_query($sql);
+  $records = chado_query($sql, $args);
   $transaction  = db_transaction();
 
+  print "\nNOTE: publishing records is performed using a database transaction. \n" .
+      "If the load fails or is terminated prematurely then the entire set of \n" .
+      "is rolled back with no changes to the database\n\n";
+
   printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, 0, number_format(memory_get_usage()));
   try {
     $i = 0;
@@ -157,8 +183,6 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
         'entity_id' => $entity->id,
         'record_id' => $record_id,
         'data_table' => $table,
-        'type_table' => $table,
-        'field' => $column,
       );
 
       // For the Tv2 to Tv3 migration we want to add the nid to the

tripal_chado/api/tripal_chado.schema.api.inc

@@ -647,7 +647,7 @@ function chado_get_cvterm_mapping($params) {
     $cvterm = chado_generate_var('cvterm', $match);
   }
 
-  $result = db_select('tripal_cvterm_mapping', 'tcm')
+  $result = db_select('chado_cvterm_mapping', 'tcm')
     ->fields('tcm')
     ->condition('cvterm_id', $cvterm->cvterm_id)
     ->execute();

tripal_chado/api/tripal_chado.variables.api.inc

@@ -151,9 +151,10 @@ function chado_generate_var($table, $values, $base_options = array()) {
   $table_desc = chado_get_schema($table);
   if (!$table_desc or count($table_desc) == 0) {
     tripal_report_error('tripal_chado', TRIPAL_ERROR,
-      "chado_generate_var: The table '%table' has not been defined. " .
+      "chado_generate_var: The table '%table' has not been defined " .
       "and cannot be expanded. If this is a custom table, please add it using the Tripal " .
-      "custom table interface.", array('%table' => $table));
+      "custom table interface. Values: %values",
+        array('%table' => $table, '%values' => print_r($values, TRUE)));
     if ($return_array) {
       return array();
     }

tripal_chado/includes/tripal_chado.entity.inc

@@ -5,7 +5,8 @@
  * Implements hook_entity_create().
  *
  * This hook is called when brand new entities are created, but
- * they are not loaded so the hook_entity_load() is not yet called.
+ * they are not loaded so the hook_entity_load() is not yet called. We
+ * can use this hook to add properties to the entity before saving.
  */
 function tripal_chado_entity_create(&$entity, $type) {
   if ($type == 'TripalEntity') {
@@ -17,18 +18,9 @@ function tripal_chado_entity_create(&$entity, $type) {
 
       // Add in the Chado table information for this entity type.
       $bundle = tripal_load_bundle_entity(array('name' => $entity->bundle));
-      $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
-      $vocab = $term->vocab;
-      $params = array(
-        'vocabulary' => $vocab->vocabulary,
-        'accession' => $term->accession,
-      );
-      $mapped_table = chado_get_cvterm_mapping($params);
-      $chado_table = $mapped_table->chado_table;
-      $chado_column = $mapped_table->chado_field;
-      if ($chado_table) {
-        $entity->chado_table = $chado_table;
-        $entity->chado_column = $chado_column;
+      if ($bundle->data_table) {
+        $entity->chado_table = $bundle->data_table;
+        $entity->chado_column = $bundle->type_column;
       }
     }
     if (!property_exists($entity, 'chado_record')) {
@@ -56,12 +48,27 @@ function tripal_chado_entity_postsave($entity, $type) {
  */
 function tripal_chado_entity_load($entities, $type) {
 
+  if ($type == 'TripalBundle') {
+    foreach ($entities as $bundle) {
+      // We want to add in the record ID to the entity.
+      if (property_exists($bundle, 'id')) {
+        $chado_bundle = db_select('chado_bundle', 'cb')
+          ->fields('cb')
+          ->condition('cb.bundle_id', $bundle->id)
+          ->execute()
+          ->fetchObject();
+        $bundle->data_table = $chado_bundle->data_table;
+        $bundle->type_linker_table = $chado_bundle->type_linker_table;
+        $bundle->type_column = $chado_bundle->type_column;
+        $bundle->type_id = $chado_bundle->type_id;
+      }
+    }
+  }
   if ($type == 'TripalEntity') {
     foreach ($entities as $entity) {
 
       // We want to add in the record ID to the entity.
       if (property_exists($entity, 'id')) {
-
         // Set some defaults on vars needed by this module.
         $entity->chado_table = NULL;
         $entity->chado_column = NULL;
@@ -73,19 +80,10 @@ function tripal_chado_entity_load($entities, $type) {
         if (!$bundle) {
           continue;
         }
-        $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
-        $vocab = $term->vocab;
-        $params = array(
-          'vocabulary' => $vocab->vocabulary,
-          'accession' => $term->accession,
-        );
-        $mapped_table = chado_get_cvterm_mapping($params);
-        $chado_table = $mapped_table->chado_table;
-        $chado_column = $mapped_table->chado_field;
-        if ($chado_table) {
-          $entity->chado_table = $chado_table;
-          $entity->chado_column = $chado_column;
-        }
+        // TODO: this may need fixing. The chado_column may not always
+        // be the type_id of the base table. Is it expected to be so here?
+        $entity->chado_table = $bundle->data_table;
+        $entity->chado_column = $bundle->type_column;
 
         $chado_entity = db_select('chado_entity' ,'ce')
           ->fields('ce')
@@ -93,8 +91,8 @@ function tripal_chado_entity_load($entities, $type) {
           ->execute()
           ->fetchObject();
         if ($chado_entity) {
-          $schema = chado_get_schema($chado_table);
-          $record = chado_generate_var($chado_table, array($schema['primary key'][0] => $chado_entity->record_id));
+          $schema = chado_get_schema($entity->chado_table);
+          $record = chado_generate_var($entity->chado_table, array($schema['primary key'][0] => $chado_entity->record_id));
           $entity->chado_record = $record;
           $entity->chado_record_id = $chado_entity->record_id;
         }
@@ -160,27 +158,14 @@ function tripal_chado_entity_access($op, $entity = NULL, $account = NULL) {
 
 /**
  * Implements hook_tripal_default_title_format().
+ *
+ * Overrides the default titles.
  */
-function tripal_chado_tripal_default_title_format($entity, $available_tokens) {
+function tripal_chado_tripal_default_title_format($bundle, $available_tokens) {
   $format = array();
 
-  // Load the bundle
-  $bundle = tripal_load_bundle_entity(array('term_id' => $entity->term_id));
-  $bundle_id = $bundle->id;
-  $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
-  $vocab = $term->vocab;
-  $params = array(
-    'vocabulary' => $vocab->vocabulary,
-    'accession' => $term->accession,
-  );
-  $mapped_table = chado_get_cvterm_mapping($params);
-  $table = $mapped_table->chado_table;
-  $column = $mapped_table->chado_field;
-  $cvterm_id = $mapped_table->cvterm->cvterm_id;
-
-  // TODO: the tables should not be hardcoded, but a the unique constraint should
-  // be used to create default titles
-  // For organism titles  we want the genus and species with no comma separation.
+  $table = $bundle->data_table;
+
   if ($table == 'organism') {
     $format[] = array(
       'format' => '[taxrank__genus] [taxrank__species]',
@@ -189,7 +174,7 @@ function tripal_chado_tripal_default_title_format($entity, $available_tokens) {
   }
   if ($table == 'analysis') {
     $format[] = array(
-      'format' => '[analysis__name]',
+      'format' => '[schema__name]',
       'weight' => -5
     );
   }
@@ -205,6 +190,12 @@ function tripal_chado_tripal_default_title_format($entity, $available_tokens) {
       'weight' => -5
     );
   }
+  if ($table == 'pub') {
+    $format[] = array(
+      'format' => '[tpub__title]',
+      'weight' => -5,
+    );
+  }
   return $format;
 }
 
@@ -288,15 +279,8 @@ function tripal_chado_entity_view($entity, $type, $view_mode, $langcode) {
 
       // Get the Chado table for this data type.
       $bundle = tripal_load_bundle_entity(array('name' => $entity->bundle));
-      $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
-      $vocab = $term->vocab;
-      $params = array(
-        'vocabulary' => $vocab->vocabulary,
-        'accession' => $term->accession,
-      );
-      $mapped_table = chado_get_cvterm_mapping($params);
-      $chado_table = $mapped_table->chado_table;
-      $chado_field = $mapped_table->chado_field;
+      $chado_table = $bundle->data_table;
+      $chado_field = $bundle->type_column;
 
       // Get the list of templates that should be used for entities and generatte
       // the key in the array for this entity type (using the chado table the

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -63,8 +63,6 @@ function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
       'entity_id' => $entity->id,
       'record_id' => $base_record_id,
       'data_table' => $base_table,
-      'type_table' => $base_table,
-      'field' => $type_field,
     );
     $success = drupal_write_record('chado_entity', $record);
     if (!$success) {
@@ -191,13 +189,18 @@ function tripal_chado_field_storage_load($entity_type, $entities, $age,
   $langcode = $language->language;
 
   foreach ($entities as $id => $entity) {
+
     if (property_exists($entity, 'chado_table')) {
       // Get the base table and record id for the fields of this entity.
       $base_table = $entity->chado_table;
       $type_field = $entity->chado_column;
       $record_id  = $entity->chado_record_id;
-    }
+   }
     else {
+      $bundle = tripal_load_bundle_entity(array('name' => $entity->bundle));
+      $base_table = $bundle->data_table;
+      $type_field = $bundle->type_column;
+
       // Get the base table and record id for the fields of this entity.
       $details = db_select('chado_entity', 'ce')
         ->fields('ce')
@@ -207,9 +210,6 @@ function tripal_chado_field_storage_load($entity_type, $entities, $age,
       if (!$details) {
         // TODO: what to do if record is missing!
       }
-      // Get some values needed for loading the values from Chado.
-      $base_table = isset($details->data_table) ? $details->data_table : '';
-      $type_field = isset($details->field) ? $details->field : '';
       $record_id  = isset($details->record_id) ? $details->record_id : '';
     }
 

tripal_chado/includes/tripal_chado.fields.inc

@@ -1,59 +1,19 @@
 <?php
 
-/**
- * Implements hook_chado_bundle_create().
- *
- * This is a Tripal hook. It allows any module to perform tasks after
- * a bundle has been created.
- *
- * @param $bundle
- *  The TripalBundle object.
- */
-
-function tripal_chado_bundle_create($bundle, $args) {
-  $entity_type = $bundle->type;
-
-  //dpm($args);
-  // Before adding fields to the bundle we need to story the Chado table that
-  // this bundle maps to.  That information is in the $args['form_values']
-  // array.  The $args['form_values'] array contains values that indicate the
-  // Chado table.
-  // TODO: we need to store the chado table and type field used for this
-  // bundle.
-
-  // Create/Add the new fields for this bundle.
-  tripal_chado_bundle_create_fields($entity_type, $bundle);
-
-  // Create/Add the new field instances for this bundle.
-  tripal_chado_bundle_create_instances($entity_type, $bundle);
-}
-
-
-
 /**
  * Implements hook_field_create_info().
  *
  * This is a Tripal defined hook that supports integration with the
  * TripalEntity field.
  */
-function tripal_chado_bundle_create_fields($entity_type, $bundle) {
-
-  // Get the table this bundle is mapped to.
-  $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
-  $vocab = $term->vocab;
-  $params = array(
-    'vocabulary' => $vocab->vocabulary,
-    'accession' => $term->accession,
-  );
-  $mapped_table = chado_get_cvterm_mapping($params);
+function tripal_chado_bundle_create_fields($entity_type, $bundle, $chado_bundle) {
 
   // Get the details about the mapping of this bundle to the Chado table:
   $details = array(
-    'chado_cv_id' => $mapped_table->cvterm->cv_id->cv_id,
-    'chado_cvterm_id' => $mapped_table->cvterm->cvterm_id,
-    'chado_table' => $mapped_table->chado_table,
-    'chado_type_table' => $mapped_table->chado_table,
-    'chado_type_column' => $mapped_table->chado_field,
+    'chado_cvterm_id' => $chado_bundle['type_id'],
+    'chado_table' => $chado_bundle['data_table'],
+    'chado_type_table' => $chado_bundle['type_linker_table'],
+    'chado_type_column' => $chado_bundle['type_column'],
   );
 
   $info = array();
@@ -93,7 +53,6 @@ function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type,
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
   $type_field = $details['chado_type_column'];
-  $cv_id      = $details['chado_cv_id'];
   $cvterm_id  = $details['chado_cvterm_id'];
 
   // Iterate through the columns of the table and see if fields have been
@@ -116,9 +75,9 @@ function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type,
     $cvterm = tripal_get_chado_semweb_term($table_name, $column_name, array('return_object' => TRUE));
     if (!$cvterm) {
       tripal_report_error('tripal', TRIPAL_ERROR,
-        'Cannot create term for "%table_name.%column_name". Missing an appropriate vocabulary term',
+        'Cannot create field for "%table_name.%column_name". Missing an appropriate vocabulary term',
          array('%table_name' => $table_name, '%column_name' => $column_name));
-      drupal_set_message(t('Cannot create term for "%table_name.%column_name". Missing an appropriate vocabulary term',
+      drupal_set_message(t('Cannot create field for "%table_name.%column_name". Missing an appropriate vocabulary term',
         array('%table_name' => $table_name, '%column_name' => $column_name)), 'error');
       continue;
     }
@@ -221,13 +180,13 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
   $type_field = $details['chado_type_column'];
-  $cv_id      = $details['chado_cv_id'];
   $cvterm_id  = $details['chado_cvterm_id'];
-  $schema = chado_get_schema($table_name);
 
+  $schema = chado_get_schema($table_name);
 
   // BASE ORGANISM_ID
-  if ($table_name != 'organism' and array_key_exists('organism_id', $schema['fields'])) {
+  if ($table_name != 'organism' and
+      array_key_exists('organism_id', $schema['fields'])) {
     $field_name = 'obi__organism';
     $field_type = 'obi__organism';
     $info[$field_name] = array(
@@ -344,7 +303,6 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
   $type_field = $details['chado_type_column'];
-  $cv_id      = $details['chado_cv_id'];
   $cvterm_id  = $details['chado_cvterm_id'];
 
   // CONTACTS
@@ -539,23 +497,13 @@ function tripal_chado_bundle_create_fields_linker(&$info, $details, $entity_type
  * This is a Tripal defined hook that supports integration with the
  * TripalEntity field.
  */
-function tripal_chado_bundle_create_instances($entity_type, $bundle) {
+function tripal_chado_bundle_create_instances($entity_type, $bundle, $chado_bundle) {
 
-  $term = tripal_load_term_entity(array('term_id' => $bundle->term_id));
-  $vocab = $term->vocab;
-  $params = array(
-    'vocabulary' => $vocab->vocabulary,
-    'accession' => $term->accession,
-  );
-  $mapped_table = chado_get_cvterm_mapping($params);
-
-  // Get the details about the mapping of this bundle to the Chado table:
   $details = array(
-    'chado_cv_id' => $mapped_table->cvterm->cv_id->cv_id,
-    'chado_cvterm_id' => $mapped_table->cvterm->cvterm_id,
-    'chado_table' => $mapped_table->chado_table,
-    'chado_type_table' => $mapped_table->chado_table,
-    'chado_type_column' => $mapped_table->chado_field,
+    'chado_cvterm_id' => $chado_bundle['type_id'],
+    'chado_table' => $chado_bundle['data_table'],
+    'chado_type_table' => $chado_bundle['type_linker_table'],
+    'chado_type_column' => $chado_bundle['type_column'],
   );
 
   tripal_chado_bundle_create_instances_base($info, $entity_type, $bundle, $details);
@@ -591,7 +539,6 @@ function tripal_chado_bundle_create_instances_base(&$info, $entity_type, $bundle
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
   $type_field = $details['chado_type_column'];
-  $cv_id      = $details['chado_cv_id'];
   $cvterm_id  = $details['chado_cvterm_id'];
 
   // Iterate through the columns of the table and see if fields have been
@@ -783,7 +730,6 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
   $type_field = $details['chado_type_column'];
-  $cv_id      = $details['chado_cv_id'];
   $cvterm_id  = $details['chado_cvterm_id'];
   $schema = chado_get_schema($table_name);
 
@@ -1038,7 +984,6 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
   $table_name = $details['chado_table'];
   $type_table = $details['chado_type_table'];
   $type_field = $details['chado_type_column'];
-  $cv_id      = $details['chado_cv_id'];
   $cvterm_id  = $details['chado_cvterm_id'];
 
   // CONTACTS
@@ -1727,4 +1672,4 @@ function tripal_chado_form_tripalbundle_form_alter(&$form, $form_state) {
         differentiate between data types is also listed above.'),
     '#weight' => 0,
   );
-}
+}

tripal_chado/includes/tripal_chado.mapping.inc

@@ -10,7 +10,7 @@ function tripal_chado_map_cvterms() {
 
   // Perform this action in a transaction
   $transaction = db_transaction();
-  print "\nNOTE: Populating of tripal_cvterm_mapping table is performed using a database transaction. \n" .
+  print "\nNOTE: Populating of chado_cvterm_mapping table is performed using a database transaction. \n" .
       "If the load fails or is terminated prematurely then the entire set of \n" .
       "insertions/updates is rolled back and will not be found in the database\n\n";
   try {
@@ -67,10 +67,10 @@ function tripal_chado_map_cvterms() {
             AND name = :name";
         $cvterm_id = chado_query($cvterm_sql, array(':dbxref_id' => $dbxref_id, ':name' => $name))->fetchField();
         if ($cvterm_id) {
-         // Check if this term is already mapped in the tripal_cvterm_mapping table
+         // Check if this term is already mapped in the chado_cvterm_mapping table
          $check_sql =
            "SELECT mapping_id
-             FROM tripal_cvterm_mapping
+             FROM chado_cvterm_mapping
              WHERE cvterm_id = :cvterm_id";
          $mapped = db_query($check_sql, array(':cvterm_id' => $cvterm_id))->fetchField();
          // If mapping does not exist and a table name matches the term name, add it
@@ -94,31 +94,31 @@ function tripal_chado_map_cvterms() {
 /*
  * Add a cvterm mapping record
  *
- * Check if the cvterm mapping record exists. If not, add it to the tripal_cvterm_mapping
+ * Check if the cvterm mapping record exists. If not, add it to the chado_cvterm_mapping
  * table
  */
 function tripal_chado_add_cvterm_mapping($cvterm_id, $tablename, $chado_field) {
   // check if the record exists
-  $record = db_select('tripal_cvterm_mapping', 'tcm')
+  $record = db_select('chado_cvterm_mapping', 'tcm')
     ->fields('tcm', array('mapping_id'))
     ->condition('cvterm_id', $cvterm_id)
     ->execute()
     ->fetchField();
-  // insert records into the tripal_cvterm_mapping table.
+  // insert records into the chado_cvterm_mapping table.
   if (!$record) {
-    db_insert('tripal_cvterm_mapping')
+    db_insert('chado_cvterm_mapping')
     ->fields(
         array(
           'cvterm_id' => $cvterm_id,
           'chado_table' => $tablename,
           'chado_field' => $chado_field
         )
-        )
-        ->execute();
+      )
+      ->execute();
   }
   // if the record exists, update the term mapping
   else {
-    db_update('tripal_cvterm_mapping')
+    db_update('chado_cvterm_mapping')
     ->fields(
         array(
           'chado_table' => $tablename,

tripal_chado/includes/tripal_chado.migrate.inc

@@ -607,7 +607,7 @@ function tripal_chado_migrate_map_types($tv2_content_types) {
  */
 function tripal_chado_migrate_selected_types($tv3_content_types) {
 
-  // Initialize the population of the tripal_cvterm_mapping table before migration.
+  // Initialize the population of the chado_cvterm_mapping table before migration.
   tripal_chado_map_cvterms();
 
   foreach ($tv3_content_types AS $tv3_content_type) {

tripal_chado/includes/tripal_chado.semweb.inc

@@ -30,6 +30,7 @@ function tripal_chado_populate_chado_semweb_table() {
   tripal_chado_populate_vocab_SCHEMA();
   tripal_chado_populate_vocab_SWO();
   tripal_chado_populate_vocab_TAXRANK();
+  tripal_chado_populate_vocab_TPUB();
 }
 
 /**
@@ -415,6 +416,38 @@ function tripal_chado_populate_vocab_SWO() {
 
 }
 
+/**
+ * Adds the pub table mapping.
+ */
+function tripal_chado_populate_vocab_TPUB() {
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000039'));
+  tripal_associate_chado_semweb_term('pub', 'title', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000243'));
+  tripal_associate_chado_semweb_term('pub', 'volumetitle', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000042'));
+  tripal_associate_chado_semweb_term('pub', 'volume', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000256'));
+  tripal_associate_chado_semweb_term('pub', 'series_name', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000043'));
+  tripal_associate_chado_semweb_term('pub', 'issue', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000059'));
+  tripal_associate_chado_semweb_term('pub', 'pyear', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000044'));
+  tripal_associate_chado_semweb_term('pub', 'pages', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000244'));
+  tripal_associate_chado_semweb_term('pub', 'publisher', $term);
+
+  $term = tripal_get_cvterm(array('id' => 'TPUB:0000245'));
+  tripal_associate_chado_semweb_term('pub', 'pubplace', $term);
+}
+
 /**
  * Adds the Taxonomic Rank Ontology database and terms.
  */

tripal_chado/includes/tripal_chado.setup.inc

@@ -409,29 +409,75 @@ function tripal_chado_prepare_chado() {
 
     // Create the 'Organism' entity type. This uses the obi:organism term.
     $error = '';
-    if (!tripal_create_bundle('OBI', '0100026', 'organism', $error)) {
+    $args = array(
+     'vocabulary' => 'OBI',
+     'accession' => '0100026',
+     'term_name' => 'organism',
+     'storage_args' => array(
+       'data_table' => 'organism',
+     )
+    );
+    if (!tripal_create_bundle($args, $error)) {
       throw new Exception($error['!message']);
     }
 
     // Create the 'Analysis' entity type. This uses the local:analysis term.
     $error = '';
-    if (!tripal_create_bundle('local', 'analysis', 'analysis', $error)) {
+    $args = array(
+      'vocabulary' => 'local',
+      'accession' => 'analysis',
+      'term_name' => 'analysis',
+      'storage_args' => array(
+        'data_table' => 'analysis',
+      )
+    );
+    if (!tripal_create_bundle($args, $error)) {
       throw new Exception($error['!message']);
     }
 
     // Create the 'Project' entity type. This uses the local:project term.
     $error = '';
-    if (!tripal_create_bundle('local', 'project', 'project', $error)) {
+    $args = array(
+      'vocabulary' => 'local',
+      'accession' => 'project',
+      'term_name' => 'project',
+      'storage_args' => array(
+        'data_table' => 'project',
+      )
+    );
+    if (!tripal_create_bundle($args, $error)) {
       throw new Exception($error['!message']);
     }
 
-    // Create the 'Project' entity type. This uses the local:project term.
+//     // Create the 'Genetic Map' entity type. This uses the local:project term.
+//     $error = '';
+//     $args = array(
+//       'vocabulary' => 'data',
+//       'accession' => '1278',
+//       'term_name' => 'Genetic map',
+//       'storage_args' => array(
+//         'data_table' => 'featuremap',
+//       )
+//     );
+//     if (!tripal_create_bundle($args, $error)) {
+//       throw new Exception($error['!message']);
+//     }
+
+    // Create the 'Publication' entity type.
     $error = '';
-    if (!tripal_create_bundle('data', '1278', 'Genetic map', $error)) {
+    $args = array(
+      'vocabulary' => 'TPUB',
+      'accession' => '0000002',
+      'term_name' => 'Publication',
+      'storage_args' => array(
+        'data_table' => 'pub',
+      )
+    );
+    if (!tripal_create_bundle($args, $error)) {
       throw new Exception($error['!message']);
     }
 
-    // Initialize the population of the tripal_cvterm_mapping table.
+    // Initialize the population of the chado_cvterm_mapping table.
     tripal_chado_map_cvterms();
 
     // Set a variable to indicate the site is prepared.

tripal_chado/includes/tripal_chado.vocab_storage.inc

@@ -7,7 +7,7 @@
 function tripal_chado_vocab_storage_info() {
   return array(
     'term_chado_storage' => array(
-      'label' => t('Chado storage'),
+      'label' => t('Chado'),
       'module' => 'tripal_chado',
       'description' => t('Integrates terms stored in the local Chado database
           with Tripal entities.'),
@@ -119,170 +119,4 @@ 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, $form_state);
-}
-/**
- * Implements hook_vocab_select_term_form().
- *
- * TODO: can't this be moved over to the tripal module and remove the
- *  Chado specific parts???
- */
-function tripal_chado_vocab_select_term_form($form, &$form_state) {
-  $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
-
-  // 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
-        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/",
-  );
-  $form['select_button'] = array(
-    '#type' => 'submit',
-    '#value' => t('Lookup Term'),
-    '#name' => 'select_cvterm',
-    '#ajax' => array(
-      'callback' => "tripal_chado_vocab_select_term_form_ajax_callback",
-      'wrapper' => "tripal-chado-vocab-select-form",
-      'effect' => 'fade',
-      'method' => 'replace'
-    ),
-  );
-
-  if ($term_name) {
-    $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');
-    $num_terms = 0;
-    foreach ($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');
-      }
-       $form['terms_list']['term-' . $term->cvterm_id] = 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,
-       );
-       $base_tables = chado_get_base_tables();
-       $default_table = 0;
-       $options = array(0 => '-- Select table --');
-       foreach ($base_tables AS $tablename) {
-         $options[$tablename] = $tablename;
-       }
-       $mapped_table = chado_get_cvterm_mapping(array('cvterm_id' => $term->cvterm_id));
-       if ($mapped_table) {
-         $default_table = $mapped_table->chado_table;
-       }
-       $form['terms_list']['default_table-' . $term->cvterm_id] = array(
-         '#type' => 'select',
-         '#title' => 'Chado table',
-         '#options' => $options,
-         '#description' => 'Select the table in Chado where data of this type
-           will be stored.',
-         '#default_value' => $default_table
-       );
-       $num_terms++;
-    }
-    if ($num_terms == 0) {
-      $form['terms_list']['none'] = array(
-        '#type' => 'item',
-        '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
-      );
-    }
-    // Add in the button for the cases of no terms or too many.
-    $form['submit_button'] = array(
-      '#type' => 'submit',
-      '#value' => t('Use this term'),
-      '#name' => 'use_cvterm'
-    );
-  }
-
-  $form['#prefix'] = '<div id = "tripal-chado-vocab-select-form">';
-  $form['#suffix'] = '</div>';
-
-  return $form;
-}
-
-/**
- * Implements an AJAX callback for the tripal_chado_vocab_select_term_form.
- */
-function tripal_chado_vocab_select_term_form_ajax_callback($form, $form_state) {
-  return $form;
-}
-
-/**
- * Implements hook_vocab_select_term_form_validate().
- */
-function tripal_chado_vocab_select_term_form_validate($form, &$form_state) {
-
-  if (array_key_exists('clicked_button', $form_state) and
-      $form_state['clicked_button']['#name'] =='use_cvterm') {
-
-    $cvterm_id = NULL;
-
-    // Make sure we have a cvterm selected
-    $num_selected = 0;
-    foreach ($form_state['values'] as $key => $value) {
-      $matches = array();
-      if (preg_match("/^term-(\d+)$/", $key, $matches) and
-          $form_state['values']['term-' . $matches[1]]) {
-        $cvterm_id = $matches[1];
-        $term = chado_generate_var('cvterm', array('cvterm_id' => $cvterm_id));
-        $num_selected++;
-      }
-    }
-    if ($num_selected == 0) {
-      form_set_error('', 'Please select at least one term.');
-    }
-    else if ($num_selected > 1) {
-      form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
-    }
-    else {
-      $form_state['storage']['vocabulary'] = $term->dbxref_id->db_id->name;
-      $form_state['storage']['accession'] = $term->dbxref_id->accession;
-      $form_state['storage']['term_name'] = $term->name;
-      // Make sure a default table is selected
-      $default_table = $form_state['values']['default_table-' . $cvterm_id];
-      if (!$default_table) {
-        form_set_error('default_table-' . $cvterm_id, 'Please select a default table.');
-      }
-      else {
-        $chado_field = NULL;
-        $schema = chado_get_schema($default_table);
-        if (isset($schema['foreign keys']['cvterm']['columns'])) {
-          $fkey = array_keys($schema['foreign keys']['cvterm']['columns']);
-          $chado_field = $fkey[0];
-        }
-        tripal_chado_add_cvterm_mapping($cvterm_id, $default_table, $chado_field);
-      }
-    }
-  }
-  // 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/tripal_chado.install

@@ -156,6 +156,7 @@ function tripal_chado_schema() {
 
   // Links TripalEntity entities to the chado record.
   $schema['chado_entity'] = tripal_chado_chado_entity_schema();
+  $schema['chado_bundle'] = tripal_chado_chado_bundle_schema();
   $schema['chado_semweb'] = tripal_chado_chado_semweb_schema();
 
   $schema['tripal_mviews'] = tripal_chado_tripal_mviews_schema();
@@ -180,7 +181,7 @@ function tripal_chado_schema() {
   }
 
   // Map cvterm usage to chado tables
-  $schema['tripal_cvterm_mapping'] = tripal_chado_tripal_cvterm_mapping_schema();
+  $schema['chado_cvterm_mapping'] = tripal_chado_chado_cvterm_mapping_schema();
 
   return $schema;
 }
@@ -584,48 +585,96 @@ function tripal_chado_chado_entity_schema() {
         'type' => 'int',
         'not null' => TRUE,
       ),
+      'data_table' => array(
+        'description' => 'The table in that this record belongs to',
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => TRUE,
+        'default' => '',
+      ),
       'record_id' => array(
         'description' => 'The unique numerical identifier for the record that this entity is associated with (e.g. feature_id, stock_id, library_id, etc.).',
         'type' => 'int',
         'not null' => TRUE,
       ),
+      'nid' => array(
+        'description' => 'Optional. For linking nid to the entity when migrating Tripal v2 content',
+        'type' => 'int',
+      )
+    ),
+    'indexes' => array(
+      'record_id' => array('record_id'),
+      'entity_id' => array('entity_id'),
+      'data_table' => array('data_table'),
+      'nid' => array('nid'),
+    ),
+    'unique keys' => array(
+      'table_record' => array('data_table', 'record_id'),
+      'entity_id' => array('entity_id'),
+    ),
+    'primary key' => array('chado_entity_id'),
+  );
+  return $schema;
+}
+
+/**
+ * Links Biological Data Entities to the chado "base" table the data is stored in.
+ * This is where we would specify that a particular gene maps to the record in the
+ * chado.feature table with a feature_id=2432;
+ */
+function tripal_chado_chado_bundle_schema() {
+
+  $schema = array(
+    'description' => 'Describes how a bundle maps data to Chado',
+    'fields' => array(
+      'chado_bundle_id' => array(
+        'description' => 'The primary identifier for this table.',
+        'type' => 'serial',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+      ),
+      'bundle_id' => array(
+        'description' => 'The unique entity id.',
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
       'data_table' => array(
-        'description' => 'Indicates the table in Chado that this term services (e.g. feature, stock, library, etc.)',
+        'description' => 'The table in Chado that this term services (e.g. feature, stock, library, etc.)',
         'type' => 'varchar',
         'length' => 128,
         'not null' => TRUE,
         'default' => '',
       ),
-      'type_table' => array(
-        'description' => 'Sometimes the record in the data table doesn’t have a field that specifies  the record type.  For example, an analysis type is stored in the analysisprop table.  If the data_table does have a type field then this value will be the same as the data_table.',
+      'type_linker_table' => array(
+        'description' => 'The table in Chado that identifies the data type. This column should be used if the data type is not specified by a "type_id" (or similar) field in the data table. The linker table must have a foreign key to the data table.',
         'type' => 'varchar',
         'length' => 128,
-        'not null' => TRUE,
+        'not null' => FALSE,
         'default' => '',
       ),
-      'field' => array(
-        'description' => 'The name of the field in the typetable that contains the cvterm record.',
+      'type_column' => array(
+        'description' => 'The column in the data table that distinguishes the data types. This must be in a foreign key relationship to the cvterm table.',
         'type' => 'varchar',
         'length' => 128,
         'not null' => FALSE,
-        'default' => ''
+        'default' => '',
+      ),
+      'type_id' => array(
+        'description' => 'If a type_column is set then this is the cvterm_id of the data type that this bundle maps to.',
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => TRUE,
+        'default' => '',
       ),
-      'nid' => array(
-        'description' => 'Optional. For linking nid to the entity when migrating Tripal v2 content',
-        'type' => 'int',
-      )
     ),
     'indexes' => array(
-      'record_id' => array('record_id'),
-      'entity_id' => array('entity_id'),
+      'bundle_id' => array('bundle_id'),
       'data_table' => array('data_table'),
-      'nid' => array('nid'),
     ),
     'unique keys' => array(
-      'record' => array('data_table', 'record_id'),
-      'entity_id' => array('entity_id'),
+      'record' => array('bundle_id'),
     ),
-    'primary key' => array('chado_entity_id'),
+    'primary key' => array('chado_bundle_id'),
   );
   return $schema;
 }
@@ -634,10 +683,10 @@ function tripal_chado_chado_entity_schema() {
  * Tripal cvterm mapping schema
  * Map cvterms to chado tables that use them
  */
-function tripal_chado_tripal_cvterm_mapping_schema() {
+function tripal_chado_chado_cvterm_mapping_schema() {
 
   $schema = array (
-    'table' => 'tripal_cvterm_mapping',
+    'table' => 'chado_cvterm_mapping',
     'fields' => array (
       'mapping_id' => array(
         'type' => 'serial',

tripal_chado/tripal_chado.module

@@ -37,6 +37,7 @@ require_once "includes/tripal_chado.entity.inc";
 require_once "includes/tripal_chado.schema.inc";
 require_once "includes/tripal_chado.vocab_storage.inc";
 require_once "includes/tripal_chado.field_storage.inc";
+require_once "includes/tripal_chado.bundle.inc";
 require_once "includes/tripal_chado.fields.inc";
 require_once "includes/tripal_chado.mapping.inc";
 

tripal_chado/views_handlers/chado_views_handler_filter.inc

@@ -421,7 +421,7 @@ function _chado_views_add_table_joins(&$handler) {
   $alias = $handler->query->add_relationship('chado_entity', $join, $handler->table_alias, $handler->relationship);
 
   // Restrict the chado_entity join to only return the table this field is from.
-  $handler->query->add_where(0, $alias .'.data_table', $handler->definition['chado_table'], '=');
+  $handler->query->add_where(0, $alias . '.data_table', $handler->definition['chado_table'], '=');
 
   // Now, we need to join from chado_entity to the chado table needed by this field.
   // This only works if the field is from the base table.

tripal_panes/tripal_panes.install

@@ -180,7 +180,6 @@ function tripal_panes_update_dependencies() {
   // site upgrade when the tripal_core module is disabled.
   //module_load_include('module', 'tripal', 'tripal');
   //tripal_import_api();
-print "HI!!!\n";
   module_load_include('module', 'tripal_ws', 'tripal_ws');
 
   $dependencies = array();