tripal/tripal_chado/includes/tripal_chado.field_storage.inc

<?php

/**
 * Implements hook_field_storage_info().
 */
function tripal_chado_field_storage_info() {
  return array(
    'field_chado_storage' => array(
      'label' => t('Chado'),
      'description' => t('Stores fields in the local Chado database.'),
      'settings' => array(
        'tripal_storage_api' => TRUE,
      ),
      // The logo_url key is supported by Tripal. It's not a Drupal key. It's
      // used for adding a logo or picture for the data store to help make it
      // more easily recognized on the  field_ui_field_overview_form. Ideally
      // the URL should point to a relative path on the local Drupal site.
      'logo_url' => url(drupal_get_path('module', 'tripal') . '/theme/images/250px-ChadoLogo.png'),
    ),
  );
}

/**
 * Implements hook_field_storage_write().
 */
function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {

  // Get the bundle and the term for this entity.
  $bundle = tripal_load_bundle_entity(array('name' => $entity->bundle));
  $term = entity_load('TripalTerm', array('id' => $entity->term_id));
  $term = reset($term);

  // Convert the Tripal term entity into the appropriate record in Chado.
  $dbxref = chado_get_dbxref(array('accession' => $term->accession, 'db_id' => array('name' => $term->vocab->vocabulary)));
  $cvterm = chado_get_cvterm(array('dbxref_id' => $dbxref->dbxref_id));

  // Get the base table, type field and record_id from the entity.
  $base_table = $entity->chado_table;
  $type_field = $entity->chado_column;
  $record = $entity->chado_record;
  $record_id = $entity->chado_record_id;
  $linker = property_exists($entity, 'chado_linker') ? $entity->chado_linker : '';
  $type_id = property_exists($entity, 'chado_type_id') ? $entity->chado_type_id : '';
  $type_value = property_exists($entity, 'chado_type_value') ? $entity->chado_type_value : '';
  $base_type_id = property_exists($entity, 'chado_base_type_id') ? $entity->chado_base_type_id : '';
  $base_schema = chado_get_schema($base_table);
  $base_pkey = $base_schema['primary key'][0];

  // Convert the fields into a key/value list of fields and their values.
  list($field_vals, $field_items) = tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $entity);
  
  // Start out with the base table fields.
  $values = $field_vals[$base_table];
  
  // First, set the pkey for the record if this is an update.
  if ($record_id) {
    $values[$base_pkey] = $record_id;
  }
  // For content types that use a type_id in the base table then we need
  // to add in the type_id value.
  elseif ($type_field and !$linker) {
    $values[$type_field] = $cvterm->cvterm_id;
  }
  // If we have a linker table and there is a base_type_id then the base
  // table requires a type_id and we need to add it in.
  elseif ($linker and $base_type_id) {
    // 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;
    $schema = chado_get_schema($base_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') {
            $base_type_column = 'type_id';
          }
        }
      }
    }
    if ($base_type_column) {
      $values[$base_type_column] = $base_type_id;
    }
  }
  
  // Insert the record into the base table and get the record ID.
  $base_record_id = tripal_chado_field_storage_write_table($base_table, $values, $base_table);
  if (!$base_record_id) {
    throw new Exception('Unable to write fields to Chado: ' . print_r($field_items, TRUE));
  }
  
  // For content types that use a linker table we need to add a record into
  // the linker table.
  if ($type_field and $linker) {
    // If this is for a property table then there will be a value.
    if ($type_value) {
      $field_vals[$linker][] = [
        $base_pkey => $base_record_id, 
        'type_id' => $type_id,
        'value' => $type_value,
      ];
    }
    // If there is no value then this is a cvterm table
    else {
      $args = array(':uniquename' => 'null');
      $sql = "
        SELECT *
        FROM {pub}
        WHERE uniquename = :uniquename
      ";
      $pub = chado_query($sql, $args)->fetchObject();
      if (!$pub) {
        throw new Exception('Unable to save record because the NULL publication is missing from the pub table. Please add a null record where the uniquename value is "null".');
      }
      $field_vals[$linker][] = [
        $base_pkey => $base_record_id,
        'cvterm_id' => $cvterm->cvterm_id,
        'pub_id' => $pub->pub_id,
      ];
    }
  }

  // If this is an insert then add the chado_entity record.
  if ($op == FIELD_STORAGE_INSERT) {
    // Add the record to the proper chado entity table
    $chado_entity_table = chado_get_bundle_entity_table($bundle);
    $record_id = db_insert($chado_entity_table)
      ->fields(array(
        'entity_id' => $entity->id,
        'record_id' => $base_record_id
      ))
      ->execute();
    if (!$record_id) {
      throw new Exception('Unable to insert new Chado entity.');
    }
  }

  // Now that we have handled the base table, we need to handle linking tables.
  foreach ($field_vals as $table_name => $details) {
    // Skip the base table as we've already dealt with it.
    if ($table_name == $base_table) {
      continue;
    }
    foreach ($details as $delta => $values) {
      $record_id = tripal_chado_field_storage_write_table($table_name, $values, $base_table, $base_pkey, $base_record_id);
    }
  }
}

/**
 * Write (inserts/updates/deletes) values for a Chado table.
 *
 * The $values array is of the same format used by chado_insert_record() and
 * chado_update_record().  However, both of those methods will use any nested
 * arrays (i.e. representing foreign keys) to select an appropriate record ID
 * that can be substituted as the value.  Here, the nested arrays are
 * either inserted or updated as well, but the choice is determined if the
 * primary key value is present.  If present an update occurs, if not present
 * then an insert occurs.
 *
 * This function is recursive and nested arrays from the lowest point of the
 * "tree" are dealt with first.
 *
 * @param $table_name
 *   The name of the table on which the insertion/update is performed.
 * @param $values
 *   The values array for the insertion.
 *
 * @throws Exception
 *
 * @return
 *   The unique record ID.
 */
function tripal_chado_field_storage_write_table($table_name, $values, $base_table, $base_pkey = NULL, $base_record_id = NULL) {
  $schema = chado_get_schema($table_name);
  $fkeys = $schema['foreign keys'];
  $pkey = $schema['primary key'][0];
  
  // Fields with a cardinality greater than 1 will often submit an
  // empty form.  We want to remove these empty submissions.  We can detect
  // them if all of the fields are empty.
  $num_empty = 0;
  foreach ($values as $column => $value) {
    if (!$value) {
      $num_empty++;
    }
  }
  if ($num_empty == count(array_keys($values))) {
    return '';
  }

  // If the primary key column has a value but all other values are empty then
  // this is a delete.
  if (array_key_exists($pkey, $values) and $values[$pkey]) {
    $num_vals = 0;
    foreach ($values as $value) {
      if ($value) {
        $num_vals++;
      }
    }
    if ($num_vals == 1) {
      $new_vals[$pkey] = $values[$pkey];
      if (!chado_delete_record($table_name, $new_vals)) {
        throw new Exception('Could not delete record from table: "' . $table_name . '".');
      }
      return '';
    }
  }

  // If the primary key column does not have a value then this is an insert.
  if (!array_key_exists($pkey, $values) or !$values[$pkey] or !isset($values[$pkey])) {

    // Before inserting, we want to make sure the record does not
    // already exist.  Using the unique constraint check for a matching record.
    $options = array('is_duplicate' => TRUE);
    $is_duplicate = chado_select_record($table_name, array('*'), $values, $options);
    if($is_duplicate) {
      $record = chado_select_record($table_name, array('*'), $values);
      return $record[0]->$pkey;
    }

    // If this table_name is a linker table then we want to be sure to add in
    // the value for the $base_record_id it it isn't set.  This would only
    // occur on an insert.
    if (array_key_exists($base_table, $fkeys) and $base_table != $table_name) {
      foreach ($fkeys[$base_table]['columns'] as $lkey => $rkey) {
        if ($rkey == $base_pkey and !array_key_exists($lkey, $values) or empty($values[$lkey])) {
          $values[$lkey] = $base_record_id;
        }
      }
    }

    // Insert the values array as a new record in the table but remove the
    // pkey as it should be set.
    $new_vals = $values;
    unset($new_vals[$pkey]);
    $record = chado_insert_record($table_name, $new_vals);
    if ($record === FALSE) {
      throw new Exception('Could not insert Chado record into table: "' . $table_name . '": ' . print_r($new_vals, TRUE));
    }
    return $record[$pkey];
  }

  // If we've made it to this point then this is an update.
  // TODO: what if the unique constraint matches another record?  That is
  // not being tested for here.
  $match[$pkey] = $values[$pkey];
  if (!chado_update_record($table_name, $match, $values)) {
    drupal_set_message("Could not update Chado record in table: $table_name.", 'error');
  }
  return $values[$pkey];
}

/**
 * Implements hook_field_storage_pre_load().
 *
 * Adds a 'chado_record' object containing the base record for the
 * entity.
 */
function tripal_chado_field_storage_pre_load($entity_type, $entities, $age,
    $fields, $options) {


  // Itereate through the entities and add in the Chado record.
  foreach ($entities as $id => $entity) {

    // Only deal with Tripal Entities.
    if ($entity_type != 'TripalEntity') {
      continue;
    }

    $record_id = NULL;
    if (property_exists($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 record id for the fields of this entity.
      $chado_entity_table = chado_get_bundle_entity_table($bundle);
      $details = db_select($chado_entity_table, 'ce')
        ->fields('ce')
        ->condition('entity_id', $entity->id)
        ->execute()
        ->fetchObject();
      if ($details) {
        $record_id  = isset($details->record_id) ? $details->record_id : '';
      }
      $entity->chado_table = $base_table;
      $entity->chado_record_id = $record_id;
      $entity->chado_column = $type_field;
    }
    if ($record_id) {
      // Get this table's schema.
      $schema = chado_get_schema($base_table);
      $pkey_field = $schema['primary key'][0];

      // Get the base record if one exists
      $columns = array('*');
      $match = array($pkey_field => $record_id);
      $record = chado_generate_var($base_table, $match);
      $entity->chado_record = $record;
    }
  }
}

/**
 * Implements hook_field_storage_load().
 *
 * Responsible for loading the fields from the Chado database and adding
 * their values to the entity.
 */
function tripal_chado_field_storage_load($entity_type, $entities, $age,
    $fields, $options) {

  $load_current = $age == FIELD_LOAD_CURRENT;
  global $language;
  $langcode = $language->language;

  foreach ($entities as $id => $entity) {
    $base_table = $entity->chado_table;
    $type_field = $entity->chado_column;
    $record_id  = $entity->chado_record_id;
    $record = $entity->chado_record;
    $schema = chado_get_schema($base_table);

    // Iterate through the entity's fields so we can get the column names
    // that need to be selected from each of the tables represented.
    $tables = array();
    foreach ($fields as $field_id => $ids) {

      // By the time this hook runs, the relevant field definitions have been
      // populated and cached in FieldInfo, so calling field_info_field_by_id()
      // on each field individually is more efficient than loading all fields in
      // memory upfront with field_info_field_by_ids().
      $field = field_info_field_by_id($field_id);
      $field_name = $field['field_name'];
      $field_type = $field['type'];
      $field_module = $field['module'];

      // Get the instance for this field.  If no instance exists then skip
      // loading of this field. This can happen when a field is deleted from
      // a bundle using the user UI form.
      // TODO: how to deal with deleted fields?
      $instance = field_info_instance($entity_type, $field_name, $entity->bundle);

      if (!$instance) {
        continue;
      }

      // Skip fields that don't map to a Chado table.
      if (!array_key_exists('settings', $instance) or
          !array_key_exists('chado_table', $instance['settings'])) {
        continue;
      }

      // Get the Chado table and column for this field.
      $field_table = $instance['settings']['chado_table'];
      $field_column = $instance['settings']['chado_column'];

      // There are only two types of fields: 1) fields that represent a single
      // column of the base table, or 2) fields that represent a linked record
      // in a many-to-one relationship with the base table.

      // Type 1: fields from base tables.
      if ($field_table == $base_table) {
        // Set an empty value by default, and if there is a record, then update.
        $entity->{$field_name}['und'][0]['value'] = '';
        if ($record and property_exists($record, $field_column)) {
          // If the field column is an object then it's a FK to another table.
          // and because $record object is created by the chado_generate_var()
          // function we must go one more level deeper to get the value
          if (is_object($record->$field_column)) {
            $fkey_column = $field_column;
            foreach($schema['foreign keys'] as $table => $fk_details) {
              foreach($fk_details['columns'] as $lfkey => $rfkey) {
                if ($lfkey == $field_column) {
                  $fkey_column = $rfkey;
                }
              }
            }
            $entity->{$field_name}['und'][0]['chado-' . $field_table . '__' . $field_column] = $record->$field_column->$fkey_column;
          }
          else {
            // For non FK fields we'll make the field value be the same
            // as the column value.
            $entity->{$field_name}['und'][0]['value'] = $record->$field_column;
            $entity->{$field_name}['und'][0]['chado-' . $field_table . '__' . $field_column] = $record->$field_column;
          }
        }

        // Allow the creating module to alter the value if desired.  The
        // module should do this if the field has any other form elements
        // that need populationg besides the value which was set above.
        tripal_load_include_field_class($field_type);
        if (class_exists($field_type) and is_subclass_of($field_type, 'TripalField')) {
          $tfield = new $field_type($field, $instance);
          $tfield->load($entity, array('record' => $record));
        }
        // For text fields that were not handled by a TripalField class we
        // want to automatically expand those fields.
        else {
          if ($schema['fields'][$field_column]['type'] == 'text') {
            $record = chado_expand_var($record, 'field', "$field_table.$field_column");
            $entity->{$field_name}['und'][0]['value'] = $record->$field_column;
            // Text fields that have a text_processing == 1 setting need a
            // special 'format' element too:
            if (array(key_exists('text_processing', $instance['settings']) and
                $instance['settings']['text_processing'] == 1)) {
              // TODO: we need a way to write the format back to the
              // instance settings if the user changes it when using the form.
              $entity->{$field_name}['und'][0]['format'] = array_key_exists('format', $instance['settings']) ? $instance['settings']['format'] : 'full_html';
            }
          }
        }
      }

      // Type 2: fields for linked records.  These fields will have any number
      // of form elements that might need populating so we'll offload the
      // loading of these fields to the field itself.
      if ($field_table != $base_table) {

        // Set an empty value by default, and let the hook function update it.
        $entity->{$field_name}['und'][0]['value'] = '';
        tripal_load_include_field_class($field_type);
        if (class_exists($field_type) && method_exists($field_type, 'load')) {
          $tfield = new $field_type($field, $instance);
          $tfield->load($entity, array('record' => $record));
        }
      }

    } // end: foreach ($fields as $field_id => $ids) {
  } // end: foreach ($entities as $id => $entity) {
}
/**
 * Merges the values of all fields into a single array keyed by table name.
 */
function tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $entity) {
  $all_fields = array();
  $base_fields = array();
  $field_items = array();

  // Iterate through all of the fields and organize them into a
  // new fields array keyed by the table name
  foreach ($fields as $field_id => $ids) {

    // Get the field name and information about it.
    $field = field_info_field_by_id($field_id);
    $field_name = $field['field_name'];
    $instance = field_info_instance('TripalEntity', $field['field_name'], $entity->bundle);

    // Some fields don't add data to
    // Chado so they don't have a table, but they are still attached to the
    // entity. Just skip these.
    if (!array_key_exists('chado_table', $instance['settings'])) {
      continue;
    }
    $chado_table = $instance['settings']['chado_table'];
    $chado_column = $instance['settings']['chado_column'];
    $base_table = $instance['settings']['base_table'];

    // Iterate through the field's items. Fields with cardinality ($delta) > 1
    // are multi-valued.
    $items = field_get_items($entity_type, $entity, $field_name);
    $temp = array();
    $field_items[$field_name] = $items;
    if (is_array($items)) {
      foreach ($items as $delta => $item) {
  
        // A field may have multiple items. The field can use items
        // indexed with "chado-" to represent values that should map directly
        // to chado tables and fields.
        $value_set = FALSE;
        foreach ($item as $item_name => $value) {
          $matches = array();
          if (preg_match('/^chado-(.*?)__(.*?)$/', $item_name, $matches)) {
            $table_name = $matches[1];
            $column_name = $matches[2];
            // If this field belongs to the base table then we just add
            // those values in... there's no delta.
            if ($table_name == $base_table) {
              $base_fields[$table_name][$column_name] = $value;
            }
            else {
              $temp[$table_name][$delta][$column_name] = $value;
            }
            $value_set = TRUE;
          }
        }
  
        // If there is no value set for the field using the
        // chado-[table_name]__[field name] naming schema then check if a 'value'
        // item is present and if so use that for the table column value.
        if (!$value_set and array_key_exists('value', $items[$delta]) and
            !is_array($items[$delta]['value'])) {
          // If this field belongs to the base table then we just add
          // those values in... there's no delta.
          if ($base_table == $chado_table) {
            $base_fields[$chado_table][$chado_column] = $item['value'];
          }
          else {
            $temp[$chado_table][$delta][$chado_column] = $item['value'];
          }
        }
      }

      // Now merge the records for this field with the $new_fields array
      foreach ($temp as $table_name => $details) {
        foreach ($details as $delta => $list) {
          $all_fields[$table_name][] = $list;
        }
      }
    }
  }

  $all_fields = array_merge($base_fields, $all_fields);
  return [$all_fields, $field_items];
}

/**
 * Implements hook_field_storage_query().
 */
function tripal_chado_field_storage_query($query) {

  // Initialize the result array.
  $result = array(
    'TripalEntity' => array()
  );

  // There must always be an entity filter that includes the bundle. Otherwise
  // it would be too overwhelming to search every table of every content type
  // for a matching field.
  if (!array_key_exists('bundle', $query->entityConditions)) {
    return $result;
  }
  $bundle = tripal_load_bundle_entity(array('name' => $query->entityConditions['bundle']));
  if (!$bundle) {
    return;
  }
  $data_table = $bundle->data_table;
  $type_column = $bundle->type_column;
  $type_id = $bundle->type_id;
  $schema = chado_get_schema($data_table);
  $pkey = $schema['primary key'][0];

  // Initialize the Query object.
  $cquery = chado_db_select($data_table, 'base');
  $cquery->fields('base', array($pkey));

  // Iterate through all the conditions and add to the filters array
  // a chado_select_record compatible set of filters.
  foreach ($query->fieldConditions as $index => $condition) {
    $field = $condition['field'];
    $field_name = $field['field_name'];
    $field_type = $field['type'];

    // Skip conditions that don't belong to this storage type.
    if ($field['storage']['type'] != 'field_chado_storage') {
      continue;
    }

    // The Chado settings for a field are part of the instance and each bundle
    // can have the same field but with different Chado mappings. Therefore,
    // we need to iterate through the bundles to get the field instances.
    foreach ($field['bundles']['TripalEntity'] as $bundle_name) {

      // If there is a bundle filter for the entity and if the field is not
      // associated with the bundle then skip it.
      if (array_key_exists('bundle', $query->entityConditions)) {
        if (strtolower($query->entityConditions['bundle']['operator']) == 'in' and
            !array_key_exists($bundle_name, $query->entityConditions['bundle']['value'])) {
          continue;
        }
        else if ($query->entityConditions['bundle']['value'] != $bundle_name) {
          continue;
        }
      }

      // Allow the field to update the query object.
      $instance = field_info_instance('TripalEntity', $field['field_name'], $bundle_name);
      if (tripal_load_include_field_class($field_type)) {
        $field_obj = new $field_type($field, $instance);
        $field_obj->query($cquery, $condition);
      }
      // If there is not a ChadoField class for this field then add the
      // condition as is.
      else {
        $alias = $field['field_name'];
        $chado_table = $instance['settings']['chado_table'];
        $base_table = $instance['settings']['base_table'];
        $bschema = chado_get_schema($base_table);
        $bpkey = $bschema['primary key'][0];

        if ($chado_table == $base_table) {
          // Get the base table column that is associated with the term
          // passed as $condition['column'].
          $base_field = chado_get_semweb_column($chado_table, $condition['column']);

          $matches = array();
          $key = $condition['value'];
          $op = array_key_exists('operator', $condition) ? $condition['operator'] : '=';
          if (preg_match('/^(.+);(.+)$/', $key, $matches)) {
            $key = $matches[1];
            $op = $matches[2];
          }

          switch ($op) {
            case 'eq':
              $op = '=';
              break;
            case 'gt':
              $op = '>';
              break;
            case 'gte':
              $op = '>=';
              break;
            case 'lt':
              $op = '<';
              break;
            case 'lte':
              $op = '<=';
              break;
            case '<>':
            case 'ne':
              $op = '!=';
              break;
            case 'LIKE':
            case 'contains':
              $op = 'LIKE';
              if (!preg_match('/\%/', $key)) {
                $key = '%' . $key . '%';
              }
              break;
            case 'NOT LIKE':              
              $op = 'NOT LIKE';
              if (!preg_match('/\%/', $key)) {
                $key = '%' . $key . '%';
              }
              break;
            case 'starts':
              $op = 'LIKE';
              $key = $key . '%';
              break;
            default:
              $op = '=';
          }
          $cquery->condition('base.' . $base_field , $key, $op);
        }
        if ($chado_table != $base_table) {
          // TODO: I don't think we'll get here because linker fields will
          // always have a custom field that should implement a query()
          // function. But just in case here's a note to handle it.
        }
      }
    }
  } // end foreach ($query->fieldConditions as $index => $condition) {

  // Now join with the chado entity table to get published records only.
  $chado_entity_table = chado_get_bundle_entity_table($bundle);
  $cquery->join($chado_entity_table, 'CE', "CE.record_id = base.$pkey");
  $cquery->join('tripal_entity', 'TE', "CE.entity_id = TE.id");
  $cquery->fields('CE', array('entity_id'));
  $cquery->fields('TE', array('bundle'));
  if (array_key_exists('start', $query->range)) {
    $cquery->range($query->range['start'], $query->range['length']);
  }
  // Make sure we only get records of the correct entity type
  $cquery->condition('TE.bundle', $query->entityConditions['bundle']['value']);

  // Iterate through all the property conditions. These will be filters
  // on the tripal_entity table.
  foreach ($query->propertyConditions as $index => $condition) {
    $cquery->condition('TE.' . $condition['column'], $condition['value']);
  }

  // If there is an entity_id filter then apply that.
  if (array_key_exists('entity_id', $query->entityConditions)) {
    $value = $query->entityConditions['entity_id']['value'];
    $op = '';
    if (array_key_exists('op', $query->entityConditions['entity_id'])) {
      $op = $query->entityConditions['entity_id']['op'];
    }
    // Handle a single entity_id
    if (!is_array($value)) {
      switch ($op) {
        case 'CONTAINS':
          $op = 'LIKE';
          $value = '%' . $value . '%';
          break;
        case 'STARTS_WITH':
          $op = 'LIKE';
          $value = $value . '%';
          break;
        case 'BETWEEN':
          // This case doesn't make sense for a single value. So, just set it
          // equal to the end.
          $op = '=';
        default:
          $op = $op ? $op : '=';
      }
    }
    // Handle multiple entitie IDs.
    else {
      switch ($op) {
        case 'CONTAINS':
          $op = 'IN';
          break;
        case 'STARTS_WITH':
          $op = 'IN';
          break;
        case 'BETWEEN':
          $op = 'BETWEEN';
        default:
          $op = 'IN';
      }
    }
    if ($op == 'BETWEEN') {
      $cquery->condition('TE.id', $value[0], '>');
      $cquery->condition('TE.id', $value[1], '<');
    }
    else {
      $cquery->condition('TE.id', $value, $op);
    }
  }

  // Now set any ordering.
  foreach ($query->order as $index => $sort) {
    // Add in property ordering.
    if ($sort['type'] == 'property') {
       // TODO: support ordering by bundle properties.
    }
    // Add in filter ordering
    if ($sort['type'] == 'field') {

      $field = $sort['specifier']['field'];
      $field_type = $field['type'];
      $field_name = $field['field_name'];

      // Skip sorts that don't belong to this storage type.
      if ($field['storage']['type'] != 'field_chado_storage') {
        continue;
      }
      $column = $sort['specifier']['column'];
      $direction = $sort['direction'];

      // The Chado settings for a field are part of the instance and each bundle
      // can have the same field but with different Chado mappings. Therefore,
      // we need to iterate through the bundles to get the field instances.
      foreach ($field['bundles']['TripalEntity'] as $bundle_name) {

        // If there is a bundle filter for the entity and if the field is not
        // associated with the bundle then skip it.
        if (array_key_exists('bundle', $query->entityConditions)) {
          if (strtolower($query->entityConditions['bundle']['operator']) == 'in' and
              !array_key_exists($bundle_name, $query->entityConditions['bundle']['value'])) {
            continue;
          }
          else if ($query->entityConditions['bundle']['value'] != $bundle_name) {
            continue;
          }
        }

        // See if there is a ChadoField class for this instance. If not then do
        // our best to order the field.
        $instance = field_info_instance('TripalEntity', $field_name, $bundle_name);
        if (tripal_load_include_field_class($field_type)) {
          $field_obj = new $field_type($field, $instance);
          $field_obj->queryOrder($cquery, array('column' => $column, 'direction' => $direction));
        }
        // There is no class so do our best to order the data by this field
        else {
          $base_table = $instance['settings']['base_table'];
          $chado_table = $instance['settings']['chado_table'];
          $table_column = chado_get_semweb_column($chado_table, $column);
          if ($table_column) {
             if ($chado_table == $base_table) {
               $cquery->orderBy('base.' . $table_column, $direction);
             }
             else {
               // TODO: how do we handle a field that doesn't map to the base table.
               // We would expect that all of these would be custom field and
               // the ChadoField::queryOrder() function would be implemented.
             }
          }
          else {
            // TODO: handle when the name can't be matched to a table column.
          }
        }
      } // end foreach ($field['bundles']['TripalEntity'] as $bundle_name) {
    } // end if ($sort['type'] == 'field') {
  } // end foreach ($query->order as $index => $sort) {
  
  
  // Only include records that are deleted.  Tripal doesn't keep track of
  // records that are deleted that need purging separately so we can do nothing
  // with this.
  if (property_exists($query, 'deleted') and $query->deleted) {
    // There won't ever be field data marked as deleted so just created a
    // condition that always evaluates to false.
    $cquery->where('1=0');
  }

  // Please keep these dpm's they help with debugging
  // dpm($cquery->__toString());
  // dpm($cquery->getArguments());

  $records = $cquery->execute();

  // If this is not a count query then return the results.
  $result = array();
  while ($record = $records->fetchObject()) {
    $ids = array($record->entity_id, 0, $record->bundle);
    $result['TripalEntity'][$record->entity_id] = entity_create_stub_entity('TripalEntity', $ids);
  }
  return $result;
}


function tripal_chado_field_storage_bundle_mapping_form_get_defaults($form, $form_state) {

  // The term for the content type should already be set in the form state.
  $term = $form_state['values']['term'];
  
  // Get the form default values.
  $default = array(
    'table' => '',
    'has_all' => '',
    'use_linker' => '',
    'use_prop' => '',
    'type_column' => '',
    'base_selected_term' => '',
    'prop_selected_term' => '',
    'prop_term_value' => '',
    'stage' => 'table-select',
  );
  
  // Get the stage.
  if (array_key_exists('chado-stage', $form_state)) {
    $default['stage'] = $form_state['chado-stage'];
  }
  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(['cvterm_id' => $term->cvterm_id]);
    if ($mapped_table) {
      $default['table'] = $mapped_table->chado_table;
    }
  }
  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'];
  }
  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'];
  }
  if (array_key_exists('chado_type_use_prop', $form_state['values'])
    and $form_state['values']['chado_type_use_prop']) {
    $default['use_prop'] = $form_state['values']['chado_type_use_prop'];
  }
  if (array_key_exists('type_column', $form_state['values'])
    and $form_state['values']['type_column']) {
    $default['type_column'] = $form_state['values']['type_column'];
  }
  if (array_key_exists('prop_term_value', $form_state['values'])
    and $form_state['values']['prop_term_value']) {
    $default['prop_term_value'] = $form_state['values']['prop_term_value'];
  } 
  if (array_key_exists('term_name1', $form_state['values'])) {
    $default['base_selected_term'] = tripal_get_term_lookup_form_result($form, $form_state, '', 1);
  }
  if (array_key_exists('term_name2', $form_state['values'])) {
    $default['prop_selected_term'] = tripal_get_term_lookup_form_result($form, $form_state, '', 2);
  }
  
  return $default;
}
/**
 * Implements hook_field_storage_bundle_mapping_form().
 *
 * This is a Tripal added hook to the field storage API.
 */
function tripal_chado_field_storage_bundle_mapping_form($form, &$form_state, $term, &$submit_disabled) {

  $selected_term_id = (is_object($term)) ? $term->cvterm_id : NULL;
  $submit_disabled = TRUE;

  // Get the form defaults values from the form state.
  $default = tripal_chado_field_storage_bundle_mapping_form_get_defaults($form, $form_state);
  
  // Initialize the form.
  $form = array();
  
  $form['selected_cvterm_id'] = array(
    '#type' => 'value',
    '#value' => $selected_term_id,
  );
  
  tripal_chado_field_storage_bundle_mapping_form_summary($form, $form_state, $default);
  
  if ($default['stage'] == 'table-select') {
    tripal_chado_field_storage_bundle_mapping_form_table_select($form, $form_state, $term, $default);
  }
  else if ($default['stage'] == 'has-all-select') {
    tripal_chado_field_storage_bundle_mapping_form_has_all_select($form, $form_state, $term, $default);
  }
  else if ($default['stage'] == 'type-select') {
    tripal_chado_field_storage_bundle_mapping_form_type_select($form, $form_state, $term, $default);
  }
  else if ($default['stage'] == 'prop-select') {
    tripal_chado_field_storage_bundle_mapping_form_prop_select($form, $form_state, $term, $default);    
  }
  else if ($default['stage'] == 'prop-settings') {
    tripal_chado_field_storage_bundle_mapping_form_prop_settings($form, $form_state, $term, $default);
  }
  else if ($default['stage'] == 'linker-select') {
    tripal_chado_field_storage_bundle_mapping_form_linker_select($form, $form_state, $term, $default);
  }
  else if ($default['stage'] == 'linker-settings') {
    tripal_chado_field_storage_bundle_mapping_form_linker_settings($form, $form_state, $term, $default);
  }
  else if ($default['stage'] == 'complete') {
    $submit_disabled = FALSE;
  }
  
  $form['chado-settings-reset'] = array(
    '#type' => 'submit',
    '#value' => t('Reset'),
    '#name' => 'chado-settings-reset',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate',
      'tripal_admin_add_type_form_validate'
    ],
  );
    
  return $form;
}

/**
 * Adds form elements for the summary of the selection.
 */
function tripal_chado_field_storage_bundle_mapping_form_summary(&$form, &$form_state, $default) {
  $rows = [];
  $headers = [];
  
  // If we're on the first step then just return, there is no summary.
  if ($default['stage'] == 'table-select') {
    return;
  }
  
  // Make sure the form values are set.
  $form['base_chado_table'] = [
    '#type' => 'value',
    '#value' => $default['table'],
  ];
  $form['chado_table_has_all'] = [
    '#type' => 'value',
    '#value' => $default['has_all'],
  ];
  $form['type_column'] = [
    '#type' => 'value',
    '#value' => $default['type_column'],
  ];
  $form['chado_type_use_prop'] = [
    '#type' => 'value',
    '#value' => $default['use_prop'],    
  ];
  $form['prop_term'] = [
    '#type' => 'value',
    '#value' => $default['prop_selected_term'],
  ];
  $form['base_term'] = [
    '#type' => 'value',
    '#value' => $default['base_selected_term'],
  ];
  $form['prop_term_value'] = [
    '#type' => 'value',
    '#value' => $default['prop_term_value'],
  ];
  $form['chado_type_use_linker'] = [
    '#type' => 'value',
    '#value' => $default['use_linker'],
  ];
  
  //
  // Add the base table row.
  //
  $rows[] = [
    [
      'data' => 'Chado Base Table',
      'header' => TRUE,
      'width' => '20%',
    ],
    $default['table'],
  ];
  //
  // Add the row indicating if all of the records are of the type.
  //
  if ($default['has_all'] == 'Yes' or $default['has_all'] == 'No') {
    
    $message = 'Yes. All records in the ' . $default['table'] . ' table are of this type.';
    if($default['has_all'] == 'No') {
      $message = 'No. All records in the ' . $default['table'] . ' table are not of this type.';
    }
    $rows[] = [
      [
        'data' => 'All are of this type?',
        'header' => TRUE,
        'width' => '20%',
      ],
      $message,
    ];
  }
  //
  // Add the row indicating if the type_column is used.
  //
  if ($default['type_column']) {
    $message = $default['type_column'];
    if ($default['type_column'] == 'none') {
      $message = 'No type column is needed.';
    }
    $rows[] = [
      [
        'data' => 'Type Column',
        'header' => TRUE,
        'width' => '20%',
      ],
      $message,
    ];
  }
  //
  // Add the row indicating that the record can be distinguished with a prop.
  //
  if ($default['use_prop']) {
    $message = 'Yes. The field is distinguishable using a property record.';
    if ($default['use_prop'] == 'No') {
      $message = 'No. The field is not distinguishable using a property record.';
    }
    $rows[] = [
      [
        'data' => 'Use a property?',
        'header' => TRUE,
        'width' => '20%',
      ],
      $message,
    ];
  }
  //
  //  Add the row for the base type for a property mapping
  //
  if ($default['use_prop'] == 'Yes' and $default['base_selected_term']) {
    $term = $default['base_selected_term'][0];
    $rows[] = [
      [
        'data' => 'Base Type',
        'header' => TRUE,
        'width' => '20%',
      ],
      $term->name . ' (' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession .')',
    ];
  }
  //
  //  Add the row for the type for a property mapping
  //
  if ($default['prop_selected_term']) {
    $term = $default['prop_selected_term'][0];
    $rows[] = [
      [
        'data' => 'Property Type',
        'header' => TRUE,
        'width' => '20%',
      ],
      $term->name . ' (' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession .')',
    ];
  }
  //
  //  Add the row for the value for a property mapping
  //
  if ($default['prop_term_value']) {
    $rows[] = [
      [
        'data' => 'Property Value',
        'header' => TRUE,
        'width' => '20%',
      ],
      $default['prop_term_value'],
    ];
  }
  //
  //  Add the row for the linker table selection
  //
  if ($default['use_linker']) {
    $message = 'Yes. The field is distinguishable using a cvterm linker table. The Content Type will be used to find records in the linker table';
    if ($default['use_linker'] == 'No') {
      $message = 'No. The field is not distinguishable using a cvterm linker table.';
    }
    $rows[] = [
      [
        'data' => 'Use a Chado cvterm linker?',
        'header' => TRUE,
        'width' => '20%',
      ],
      $message,
    ];
  }
  
  //
  //  Add the row for the base type for a property mapping
  //
  if ($default['use_linker'] == 'Yes' and $default['base_selected_term']) {
    $term = $default['base_selected_term'][0];
    $rows[] = [
      [
        'data' => 'Base Type',
        'header' => TRUE,
        'width' => '20%',
      ],
      $term->name . ' (' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession .')',
    ];
  }
  
  $table = array(
    'header' => $headers,
    'rows' => $rows,
    'attributes' => array(
    ),
    'sticky' => FALSE,
    'caption' => '',
    'colgroups' => array(),
    'empty' => '',
  );
  
  $form['chado_settings_summary'] = [
    '#type' => 'markup',
    '#markup' => theme_table($table),
    '#weight' => -100,
  ];
  
  if ($default['stage'] == 'complete') {
    $form['im_ready'] = [
      '#type' => 'markup',
      '#markup' => '<p>Your content type is ready for creation! Please click the "Create Content Type" button below.</p>',
    ];
  }
  if ($default['stage'] == 'stop') {
    $form['im_ready'] = [
      '#type' => 'markup',
      '#markup' => '<p>Unfortunately, it is not possible to create this conent type. Please check your selections above. If you need help creating a content type, you may reach out to the Tripal Community for assistance.</p>',
    ];
  }
}

/**
 * Adds form elements for Chado table selection step
 */
function tripal_chado_field_storage_bundle_mapping_form_table_select(&$form, &$form_state, $term, $default) {

  $base_tables = chado_get_base_tables();
  $options = array(0 => '-- Select table --');
  foreach ($base_tables AS $tablename) {
    $options[$tablename] = $tablename;
  }
  $form['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-add-type-form",
      'effect' => 'fade',
      'method' => 'replace'
    ),
  );
  $form['table-select-continue'] = array(
    '#type' => 'submit',
    '#value' => t('Continue'),
    '#name' => 'chado-table-select-continue',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate',
      'tripal_admin_add_type_form_validate'
    ],
  );
}
  

/**
 * Adds form elements for step 1: Chado type field selection.
 */
function tripal_chado_field_storage_bundle_mapping_form_has_all_select(&$form, &$form_state, $term, $default) {

  // Get the schema for this table.
  $schema = chado_get_schema($default['table']);

  // If the selected base table is 'cvterm' then handle it specially.
  if ($default['table'] == 'cvterm') {
    tripal_chado_field_storage_bundle_mapping_form_add_cvterm($form,
        $form_state, $term, $default);
    if ($default['use_cvterm'] == 'cv' and $default['cv_id']) {
      $submit_disabled = FALSE;
    }
    if ($default['use_cvterm'] == 'parent') {
      $submit_disabled = FALSE;
    }
    return;
  }

  $term_name = $term->name;
  
  // Form elements to determine if all records in base table are of this type.
  $form['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 "No" if the "' .
      $default['table'] . '" table houses more than just data of type "' .
      $term_name . '".',
    '#default_value' => $default['has_all'],
  );
  
  $form['chado-has-all-select-continue'] = array(
    '#type' => 'submit',
    '#value' => t('Continue'),
    '#name' => 'chado-has-all-select-continue',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate', 
      'tripal_admin_add_type_form_validate'
    ],    
  );
}
/*
  // If all the records in the table are of this type then we're done.
  if ($default['has_all'] == 'Yes') {
    $submit_disabled = FALSE;
    return $form;
  }

  // If this table has a field that maps to a cvterm record then we want
  // to ask if the user wants to use that field.
  tripal_chado_field_storage_bundle_mapping_form_add_type($form,
      $form_state, $term, $default);

  // 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']) and $default['type_column'] != 'none') {
    $submit_disabled = FALSE;
    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';
  $linker_exists = chado_table_exists($linker_table);
  $prop_exists = chado_table_exists($prop_table);

  // Ask the user if they want to use a linker table if it exists.
  if ($prop_exists) {

    tripal_chado_field_storage_bundle_mapping_form_add_prop($form,
        $form_state, $term, $prop_table, $default);

    // If the user wants to use the property table then we're done!
    if ($default['use_prop'] == 'Yes') {
      $submit_disabled = FALSE;
      return $form;
    }

    // Ask if the user wants to use the linker table if it exists.
    if ($linker_exists) {
      tripal_chado_field_storage_bundle_mapping_form_add_linker($form,
          $form_state, $term, $linker_table, $default);

      // If the user wants to use the linker table then we're done!
      if ($default['use_linker'] == 'Yes') {
        $submit_disabled = FALSE;
        return $form;
      }
    }

  }
  // A prop table doesn't exist then ask the user if they want
  // to use the linker table to associate records.
  else if ($linker_exists) {
    tripal_chado_field_storage_bundle_mapping_form_add_prop($form,
        $form_state, $term, $prop_table, $default);

    // If the user wants to use the linker table then we're done!
    if ($default['use_linker'] == 'Yes') {
      $submit_disabled = FALSE;
      return $form;
    }
  }

  $form['notice'] = array(
    '#type' => 'item',
    '#markup' => '<font color="red">Unfortunately, the options selected above do not allow for mapping of this content type to records in Chado.</font>'
  );
  return $form;
}
 */

/**
 * Adds form elements for step 1: Chado type field selection.
 */
function tripal_chado_field_storage_bundle_mapping_form_type_select(&$form, &$form_state, $term, $default) {
  
  $term_name = $term->name;  
  $column_options = tripal_chado_field_storage_bundle_mapping_form_get_type_fks_options($default['table']);
  
  $default_column = !empty($default['type_column']) ? $default['type_column'] : 'type_id';
   
  $form['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 . '". If you select "--None--" then you will be asked
      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
  );
  $form['chado-type-select-continue'] = array(
    '#type' => 'submit',
    '#value' => t('Continue'),
    '#name' => 'chado-type-select-continue',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate',
      'tripal_admin_add_type_form_validate'
    ],
  );
}

/**
 *
 */
function tripal_chado_field_storage_bundle_mapping_form_prop_select(&$form, &$form_state, $term, $default) {
  
  $prop_table = $default['table']. 'prop';
  
  $form['chado_type_use_prop'] = array(
    '#type' => 'radios',
    '#title' => 'Do you want to use the "' . $prop_table . '" table
      to distinguish between content types?',
    '#options' => array(
      'Yes' => 'Yes',
      'No' => 'No'
    ),
    '#description' => t('Sometimes records can be distringuished
      using a value in property table, especially if there is no column
      in the specified Chado table to identify the
      record type. In these cases the property table can be used.'),
    '#default_value' => $default['use_prop'],
  );
  $form['chado-prop-select-continue'] = array(
    '#type' => 'submit',
    '#value' => t('Continue'),
    '#name' => 'chado-prop-select-continue',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate',
      'tripal_admin_add_type_form_validate'
    ],
  );
}

function tripal_chado_field_storage_bundle_mapping_form_prop_settings(&$form, &$form_state, $term, $default){
  
  $prop_term_value = $default['prop_term_value'];
  
  $base_type_column = tripal_chado_field_storage_bundle_mapping_form_get_base_type_column($default['table']);
  
  $validate =[
    'tripal_chado_field_storage_bundle_mapping_form_validate',
    'tripal_admin_add_type_form_validate'
  ];
  
  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'] . ' table requires
      that a value be given for the ' . $base_type_column . '. Please indicate
      what this type should be.  For example, suppose this content type is a SNP (SO:0000694) and
      you store SNPs in Chado in the feature table as "genetic_marker" (SO:0001645), however
      the record is defined as a SNP through a corresponding record in the featurprop
      table that has a type of "type" (rdfs:type) and a value of "SNP".
      In this case the content type should be SNP (SO:0001645) and here the
      "genetic_marker" (SO:0001645) term should be provided. The "type" term
      should be used in the Property Type field below and "SNP" as the Property Value.');
    tripal_get_term_lookup_form($form, $form_state, '',
      'Base Type', $description, FALSE, '', 1,
      'tripal_admin_add_type_form_ajax_callback', 'tripal-add-type-form', 
      $validate, -2);
  }
  
  // We need a term lookup form for the property type.
  $description = t('The content type "' . $term->name . '" must be
        associated with a property type.  The property type must be the
        name of a term in a controlled vocabulary and the controlled
        vocabulary should already be loaded into Tripal. Please select
        the property type that will be used to identify records of this
        type');
  tripal_get_term_lookup_form($form, $form_state, '',
    'Property Type', $description, FALSE, '', 2,
    'tripal_admin_add_type_form_ajax_callback', 'tripal-add-type-form', 
    $validate, -8);
  
  $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,
  );
  $form['chado-prop-settings-continue'] = array(
    '#type' => 'submit',
    '#value' => t('Continue'),
    '#name' => 'chado-prop-settings-continue',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate',
      'tripal_admin_add_type_form_validate'
    ],
  );
}

/**
 * 
 */
function tripal_chado_field_storage_bundle_mapping_form_linker_select(&$form, &$form_state, $term, $default) {
  $linker_table = $default['table'] . '_cvterm';
  $form['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 distringuished
      using a linker table, especially if there is no column
      in the specified Chado table to identify the
      record type. In these cases the linker table can be used.'),
    '#default_value' => $default['use_linker'],
  );
  $form['chado-linker-select-continue'] = array(
    '#type' => 'submit',
    '#value' => t('Continue'),
    '#name' => 'chado-linker-select-continue',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate',
      'tripal_admin_add_type_form_validate'
    ],
  );
}

/**
 * 
 */
function tripal_chado_field_storage_bundle_mapping_form_linker_settings(&$form, &$form_state, $term, $default){
    
  $base_type_column = tripal_chado_field_storage_bundle_mapping_form_get_base_type_column($default['table']);
  
  $validate =[
    'tripal_chado_field_storage_bundle_mapping_form_validate',
    'tripal_admin_add_type_form_validate'
  ];
  
  $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 cvterm linker table.  However, the ' . $default['table'] . ' table requires
    that a value be given for the ' . $base_type_column . '. Please indicate
    what this type should be.');
  tripal_get_term_lookup_form($form, $form_state, '',
    'Base Type', $description, FALSE, '', 1,
    'tripal_admin_add_type_form_ajax_callback', 'tripal-add-type-form',
    $validate, -10);
  
  $form['chado-linker-settings-continue'] = array(
    '#type' => 'submit',
    '#value' => t('Continue'),
    '#name' => 'chado-linker-settings-continue',
    '#validate' => [
      'tripal_chado_field_storage_bundle_mapping_form_validate',
      'tripal_admin_add_type_form_validate'
    ],
  );
}

/**
 * 
 */
function tripal_chado_field_storage_bundle_mapping_form_get_type_fks_options($table) {
  // Get the list of columns in the default table.
  $schema = chado_get_schema($table);
  $column_options = array('none' => '--None--');
  $cvt_fkeys = (isset($schema['foreign keys']['cvterm'])) ? array_keys($schema['foreign keys']['cvterm']['columns']) : array();
  foreach ($schema['fields'] as $column_name => $column_details) {
    if (in_array($column_name, $cvt_fkeys)) {
      $column_options[$column_name] = $column_name;
    }
  }
  return $column_options;
}
/**
 * 
 */
function tripal_chado_field_storage_bundle_mapping_form_get_base_type_column($table) {
  
  // 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;
  $schema = chado_get_schema($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';
        }
      }
    }
  }
  return $base_type_column;
}

/**
 * Implements hook_field_stoage_bundle_mapping_form_validate().
 */
function tripal_chado_field_storage_bundle_mapping_form_validate($form, &$form_state) {
  
  // Don't do validation on an ajax callback.
  if (array_key_exists('#ajax', $form_state['triggering_element'])) {
    return;
  }
  
  // Get the form values.
  $default = tripal_chado_field_storage_bundle_mapping_form_get_defaults($form, $form_state);  
  $clicked_button = $form_state['clicked_button']['#name'];

  // Check if prop  and linker tables exist. We'll use these values later.
  $prop_table = $default['table'] . 'prop';
  $prop_exists = chado_table_exists($prop_table);
  $linker_table = $default['table'] . '_cvterm';
  $linker_exists = chado_table_exists($linker_table);
  
  //
  // Valiate the table select stage
  //
  if ($clicked_button == 'chado-table-select-continue') { 
    // Make sure a default table is selected
    if (!$default['table']) {
      form_set_error('base_chado_table', 'Please select a default table.');
      return;
    }
    $form_state['chado-stage'] = 'has-all-select';
  }
  
  //
  // Valiate the has all select stage
  //
  if ($clicked_button == 'chado-has-all-select-continue') {
    if ($default['has_all'] == 'Yes') {
      $form_state['chado-stage'] = 'complete';
    }
    else {
      $column_options = tripal_chado_field_storage_bundle_mapping_form_get_type_fks_options($default['table']);      
      // If this table has fields that link to the cvterm table then 
      // let the user select the type column. The column_options is empty if
      // it equals 1 because it has the --none-- element.
      if (count($column_options) > 1) {
        $form_state['chado-stage'] = 'type-select';
      }
      // Otherwise, see if there are other options....
      else {
        // If there is no type_id or the type_id column should not be
        // used then we need to let the user select if they want to
        // use the prop table or a cvterm linking table. We'll offer the
        // prop table first.
        if ($prop_exists) {
          $form_state['chado-stage'] = 'prop-select';
        }
        else {
          if ($linker_exists) {
            $form_state['chado-stage'] = 'linker-select';
          }
          else {
            $form_state['chado-stage'] = 'stop';
          }
        }
      }

    }
  }
  
  //
  // Valiate the type select stage
  //  
  if ($clicked_button == 'chado-type-select-continue') {
    if ($default['type_column'] != 'none') {
      $form_state['chado-stage'] = 'complete';
    }
    else {
      // If there is no type_id or the type_id column should not be
      // used then we need to let the user select if they want to 
      // use the prop table or a cvterm linking table. We'll offer the
      // prop table first.
      if ($prop_exists) {
        $form_state['chado-stage'] = 'prop-select';
      }
      else {
        if ($linker_exists) {
          $form_state['chado-stage'] = 'linker-select';
        }
        else {
          $form_state['chado-stage'] = 'stop';          
        }
      }
    }
  }
  
  //
  // Valiate the property select stage
  //
  if ($clicked_button == 'chado-prop-select-continue') {
    if ($default['use_prop'] == 'Yes') {
      $form_state['chado-stage'] = 'prop-settings';
    }
    else if ($default['use_prop'] == 'No') {
      if ($linker_exists) {
        $form_state['chado-stage'] = 'linker-select';      
      }
      else {
        $form_state['chado-stage'] = 'stop';
      }
    }
    else {
      form_set_error('chado_type_use_prop', 'Please select a value.');
    }
    
  }
  
  // 
  // Validate the property settings stage
  // 
  if ($clicked_button == 'chado-prop-settings-continue') {
    // If a base type was needed then make sure we have a value selected.
    $valid = TRUE;
    if (array_key_exists('term_name1', $form_state['values'])) {
      $base_selected = $default['base_selected_term'];
      if (count($base_selected) == 0) {
        form_set_error('term_match1][term_name1', 'Please select a base table type vocabulary term.');
        $valid = FALSE;
      }
      if (count($base_selected) > 1) {
        form_set_error('term_match1][term_name1', 'Please select only one base table type vocabulary term.');
        $valid = FALSE;
      }
    }
    // Make sure we only have one property type selected
    $prop_selected = $default['prop_selected_term'];
    if (count($prop_selected) == 0) {
      form_set_error('term_match2][term_name2', 'Please select a prpoerty type vocabulary term.');
      $valid = FALSE;
    }
    if (count($prop_selected) > 1) {
      form_set_error('term_match2][term_name2', 'Please select only one property type vocabulary term.');
      $valid = FALSE;
    }
    if (!$default['prop_term_value']) {
      form_set_error('prop_term_value', 'Please provide a property value.');
      $valid = FALSE;
    }
    if (!$valid) {
      return;
    }
    // If we're here then alll validations passed and we are good to go!
    $form_state['chado-stage'] = 'complete';
  }
  
  //
  // Validate the linker settings stage
  //
  if ($clicked_button == 'chado-linker-select-continue') {
    if ($default['use_linker'] == 'Yes') {
      // If our base table has a type_id then we need need to make the 
      // user provide a value for it, otherwise we're done.
      $base_type_column = tripal_chado_field_storage_bundle_mapping_form_get_base_type_column($default['table']);
      if ($base_type_column) {
        $form_state['chado-stage'] = 'linker-settings';
      }
      else {
        $form_state['chado-stage'] = 'complete';
      }
    }
    else if ($default['use_linker'] == 'No') {
      $form_state['chado-stage'] = 'stop';
    }
    else {
      form_set_error('chado_type_use_linker', 'Please select a value.');
    }
  }
  
  if ($clicked_button == 'chado-linker-settings-continue') {
    $valid = TRUE;
    if (array_key_exists('term_name1', $form_state['values'])) {
      $base_selected = $default['base_selected_term'];
      if (count($base_selected) == 0) {
        form_set_error('term_match1][term_name1', 'Please select a base table type vocabulary term.');
        $valid = FALSE;
      }
      if (count($base_selected) > 1) {
        form_set_error('term_match1][term_name1', 'Please select only one base table type vocabulary term.');
        $valid = FALSE;
      }
    }
    if (!$valid) {
      return;
    }
    // If we're here then alll validations passed and we are good to go!
    $form_state['chado-stage'] = 'complete';
  }
  
 
  //
  // Check for a reset.
  //
  if ($clicked_button == 'chado-settings-reset') {
    $form_state['chado-stage'] = 'table-select';
    $valid = FALSE;
  }

}
/**
 * Implements hook_field_stoage_bundle_mapping_form_submit().
 *
 * Here we do no action on submit other than set the storage_args
 * variable that is passed by reference.
 */
function tripal_chado_field_storage_bundle_mapping_form_submit($form,
    &$form_state, $term, &$storage_args) {

  $default = tripal_chado_field_storage_bundle_mapping_form_get_defaults($form, $form_state);
  
  // If we have a type_column then we know this type uses a column in the
  // base table, so we can set the storage args and return.
  if ($default['type_column'] and $default['type_column'] != 'none') {
    $storage_args['data_table'] = $default['table'];
    $storage_args['type_column'] = $default['type_column'];
    return;
  }

  // If the user indicated that all the records in a table are of this type.
  if ($default['has_all'] == 'Yes') {
    $storage_args['data_table'] = $default['table'];
    $storage_args['type_id'] = $form_state['values']['selected_cvterm_id'];
    $storage_args['type_linker_table'] = '';
    $storage_args['type_column'] = '';
    $storage_args['type_value'] = '';
  }

  // If the user indicated they wanted to use the prop table then we'll
  // set the storage args and return.
  else if ($default['use_prop'] == 'Yes') {
    $storage_args['data_table'] = $default['table'];
    $storage_args['type_linker_table'] = $default['table'] . 'prop';
    $storage_args['type_column'] = 'type_id';
    $storage_args['type_id'] = $form_state['values']['prop_term'][0]->cvterm_id;
    $storage_args['type_value'] = $default['prop_term_value'];
    if (is_array($form_state['values']['base_term'])) {
      $storage_args['base_type_id'] = $form_state['values']['base_term'][0]->cvterm_id;
    }
  }

  // If the user indicated they wanted to use the linker tables then we'll
  // set the storage args and return.
  else if ($default['use_linker'] == 'Yes') {
    $storage_args['data_table'] = $default['table'];
    $storage_args['type_id'] = $form_state['values']['selected_cvterm_id'];
    $storage_args['type_linker_table'] = $default['table'] . '_cvterm';
    $storage_args['type_column'] = 'cvterm_id';
    if (is_array($form_state['values']['base_term'])) {
      $storage_args['base_type_id'] = $form_state['values']['base_term'][0]->cvterm_id;
    }
  }
}