tripal/tripal_chado/api/tripal_chado.variables.api.inc

<?php

/**
 * @file
 * This API generates objects containing the full details of a record(s) in
 *   chado.
 *
 * @ingroup tripal_chado
 */
/**
 * @defgroup tripal_chado_variables_api Semantic Web
 * @ingroup tripal_chado_api
 *
 * @{
 * This API generates objects containing the full details of a record(s) in
 *   chado.
 * @}
 */

/**
 * Generates an object containing the full details of a record(s) in Chado.
 *
 * The object returned contains key/value pairs where the keys are the fields
 * in the Chado table.
 *
 * The returned object differs from the array returned by chado_select_record()
 * as all foreign key relationships in the Chado table have been followed and
 * those data are also included. This function automatically excludes some
 * fields and tables. Fields that are extremely long, such as text fields are
 * automatically excluded to prevent long page loads.  Linking tables that have
 * a many-to-one relationship with the record are also excluded. Use the
 * chado_expand_var() to manually add in excluded fields and data from linker
 * tables.
 *
 * Example Usage:
 *
 * @code
 *   $values = array(
 *     'name' => 'Medtr4g030710'
 *   );
 *   $feature = chado_generate_var('feature', $values);
 * @endcode
 *
 * The $values array passed to this function can be of the same format used
 * by the chado_select_record() function.
 *
 * If a field is a foreign key then its value is an object that contains
 * key/value pairs for that record.  The following code provides examples
 * for retrieving values associated with the record, either as columns in the
 * original Chado table or as columns in linked records through foreign keys:
 * @code
 *   // Get the feature name.
 *   $name = $feature->name;
 *   // Get the feature unique name.
 *   $uniquename = $feature->uniquename;
 *   // Get the feature type. Because the type name is obtained via
 *   // a foreign key with the cvterm table, the objects are nested
 *   // and we can follow the foreign key fields to retrieve those values
 *   $type = $feature->type_id->name;
 *   // Get the name of the vocabulary.
 *   $cv = $feature->type_id->cv_id->name;
 *   // Get the vocabulary id.
 *   $cv_id = $feature->type_id->cv_id->cv_id;
 * @endcode
 *
 *
 * This will return an object if there is only one feature with the name
 * Medtr4g030710 or it will return an array of feature objects if more than one
 * feature has that name.
 *
 * Note to Module Designers: Fields can be excluded by default from these
 * objects by implementing one of the following hooks:
 *  - hook_exclude_field_from_tablename_by_default (where tablename is the
 *    name of the table): This hook allows you to add fields to be excluded
 *    on a per table basis. Simply implement this hook to return an array of
 *    fields to be excluded. The following example will ensure that
 *    feature.residues is excluded from a feature object by default:
 * @code
 *      mymodule_exclude_field_from_feature_by_default() {
 *        return array('residues' => TRUE);
 *      }
 * @endcode
 *  - hook_exclude_type_by_default:
 *      This hook allows you to exclude fields using conditional. This
 *      function should return an array of postgresql types mapped to criteria.
 *      If the field types of any table match the criteria then the field
 *      is excluded. Tokens available in criteria are &gt;field_value&lt;
 *      and &gt;field_name&lt;. The following example will exclude all text
 *      fields with a length > 50. Thus if $feature.residues is longer than
 *      50 it will be excluded, otherwise it will be added.
 * @code
 *        mymodule_exclude_type_by_default() {
 *          return array('text' => 'length(&gt;field_value&lt; ) > 50');
 *        }
 * @endcode
 *
 *
 * @param $table
 *   The name of the base table to generate a variable for
 * @param $values
 *   A select values array that selects the records you want from the base table
 *   (this has the same form as chado_select_record)
 * @param $base_options
 *   An array containing options for the base table.  For example, an
 *   option of 'order_by' may be used to sort results in the base table
 *   if more than one are returned.  The options must be compatible with
 *   the options accepted by the chado_select_record() function.
 *   Additionally,  These options are available for this function:
 *   -return_array:
 *     can be provided to force the function to always return an array. Default
 *     behavior is to return a single record if only one record exists or to
 *     return an array if multiple records exist.
 *  - include_fk:
 *     an array of FK relationships to follow. By default, the
 *     chado_select_record function will follow all FK relationships but this
 *     may generate more queries then is desired slowing down this function
 *     call when there are lots of FK relationships to follow.  Provide an
 *     array specifying the fields to include.  For example, if expanding a
 *     property table (e.g. featureprop) and you want the CV and accession
 *     but do not want the DB the following array would work:
 *
 *        $table_options =  array(
 *          'include_fk' => array(
 *            'type_id' => array(
 *              'cv_id' => 1,
 *              'dbxref_id' => 1,
 *            )
 *          )
 *        );
 *
 *     The above array will expand the 'type_id' of the property table but only
 *     further expand the cv_id and the dbxref_id and will go no further.
 *   - pager:
 *     Use this option if it is desired to return only a subset of results
 *     so that they may be shown within a Drupal-style pager. This should be
 *     an array with two keys: 'limit' and 'element'.  The value of 'limit'
 *     should specify the number of records to return and 'element' is a
 *     unique integer to differentiate between pagers when more than one
 *     appear on a page.  The 'element' should start with zero and increment by
 *     one for each pager.
 *
 * @return
 *   Either an object (if only one record was selected from the base table)
 *   or an array of objects (if more than one record was selected from the
 *   base table). If the option 'return_array' is provided the function
 *   always returns an array.
 *
 * @ingroup tripal_chado_variables_api
 */
function chado_generate_var($table, $values, $base_options = []) {
  $all = new stdClass();

  $return_array = 0;
  if (array_key_exists('return_array', $base_options)) {
    $return_array = 1;
  }
  $include_fk = FALSE;
  if (array_key_exists('include_fk', $base_options)) {
    $include_fk = $base_options['include_fk'];
  }
  $pager = [];
  if (array_key_exists('pager', $base_options)) {
    $pager = $base_options['pager'];
  }
  // get description for the current table-------------------------------------
  $table_desc = chado_get_schema($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 " .
      "and cannot be expanded. If this is a custom table, please add it using the Tripal " .
      "custom table interface. Values: %values",
      ['%table' => $table, '%values' => print_r($values, TRUE)]);
    if ($return_array) {
      return [];
    }
    return FALSE;
  }
  $table_primary_key = $table_desc['primary key'][0];
  $table_columns = array_keys($table_desc['fields']);

  // Expandable fields without value needed for criteria-----------------------
  // Add in the default expandable arrays
  // These are used for later expanding fields, tables, foreign keys and nodes
  $all->expandable_fields = [];
  $all->expandable_foreign_keys = [];
  if (array_key_exists('referring_tables', $table_desc) and $table_desc['referring_tables']) {
    $all->expandable_tables = $table_desc['referring_tables'];
  }
  else {
    $all->expandable_tables = [];
  }
  $all->expandable_nodes = [];


  // Get fields to be removed by name.................................
  // This gets all implementations of hook_exclude_field_from_<table>_by_default()
  // where <table> is the current table a variable is being created for.

  // This allows modules to specify that some fields should be excluded by default
  // For example, tripal core provides a tripal_chado_exclude_field_from_feature_by_default()
  // which says that we usually don't want to include the residues field by 
  // default since it can be very large and cause performance issues.

  // If a field is excluded by default it can always be expanded at a later 
  // point by calling chado_expand_var($chado_var, 'field', 
  // <field name as shown in expandable_fields array>);

  // First get an array of all the fields to be removed for the current table
  // module_invoke_all() is drupal's way of invoking all implementations of the 
  // specified hook and merging all of the results.

  // $fields_to_remove should be an array with the keys matching field names
  // and the values being strings to be executed using php_eval() to determine 
  // whether to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
  $fields_to_remove = module_invoke_all('exclude_field_from_' . $table . '_by_default');

  // Now, for each field to be removed
  foreach ($fields_to_remove as $field_name => $criteria) {

    //Replace <field_name> with the current field name
    $field_name_safe = preg_replace("/\'\"\\\/", '\\1', $field_name);
    $criteria = preg_replace('/<field_name> /', $field_name_safe, $criteria);
    // If field_value needed we can't deal with this field yet.
    if (preg_match('/<field_value> /', $criteria)) {
      break;
    }

    // If criteria then remove from query
    // @coder-ignore: only module designers can populate $criteria -not a 
    // security risk.
    $success = php_eval('<?php return ' . $criteria . '; ?>');
    if ($success) {
      unset($table_columns[array_search($field_name, $table_columns)]);
      unset($fields_to_remove[$field_name]);
      $all->expandable_fields[] = $table . '.' . $field_name;
    }
  }

  // Get fields to be removed by type................................
  // This gets all implementations of hook_exclude_type_by_default().

  // This allows modules to specify that some types of fields should be excluded 
  // by default For example, tripal core provides a 
  // tripal_chado_exclude_type_by_default() which says that text fields are 
  // often very large and if they are longer than 250 characters then
  // we want to exclude them by default

  // If a field is excluded by default it can always be expanded at a later 
  // point by calling chado_expand_var($chado_var, 'field', 
  //<field name as shown in expandable_fields array>);

  // First get an array of all the types of fields to be removed for the current
  // table module_invoke_all() is drupal's way of invoking all implementations 
  // of the specified hook and merging all of the results.

  // $types_to_remove should be an array with the keys matching field names
  // and the values being strings to be executed using php_eval() to determine 
  // whether to exclude the field (evaluates to TRUE) or not (evaluates to FALSE)
  // (ie: array('text' => 'strlen("<field_value> ") > 100');
  $types_to_remove = module_invoke_all('exclude_type_by_default');

  // Get a list of all the types of fields
  // the key is the type of field and the value is an array of fields of this 
  // type.
  $field_types = [];
  foreach ($table_desc['fields'] as $field_name => $field_array) {
    $field_types[$field_array['type']][] = $field_name;
  }

  // We want to use the types to remove in conjunction with our table field 
  // descriptions to determine which fields might need to be removed.
  foreach ($types_to_remove as $field_type => $criteria) {

    // If there are fields of that type to remove.
    if (isset($field_types[$field_type])) {

      // Do any processing needed on the php criteria
      //replace <field_name>  with the current field name.
      $field_name_safe = preg_replace('/\'|"|\\\/', '\\1', $field_name);
      $criteria = preg_replace('/<field_name> /', $field_name_safe, $criteria);
      foreach ($field_types[$field_type] as $field_name) {
        // if field_value needed we can't deal with this field yet
        if (preg_match('/<field_value>/', $criteria)) {
          $fields_to_remove[$field_name] = $criteria;
          continue;
        }

        // If criteria then remove from query
        // (as long as <field_value> is not needed for the criteria to be 
        // evaluated) @coder-ignore: only module designers can populate 
        //$criteria -not a security risk.
        $success = php_eval('<?php return ' . $criteria . '; ?>');
        if ($success) {
          unset($table_columns[array_search($field_name, $table_columns)]);
          $all->expandable_fields[] = $table . '.' . $field_name;
        }
      } // End of foreach field of that type.
    }
  } // End of foreach type to be removed.

  // Get the values for the record in the current table-------------------------
  $results = chado_select_record($table, $table_columns, $values, $base_options);

  if ($results) {

    // Iterate through each result.
    foreach ($results as $key => $object) {

      // Add empty expandable_x arrays.
      $object->expandable_fields = $all->expandable_fields;
      $object->expandable_foreign_keys = $all->expandable_foreign_keys;
      $object->expandable_tables = $all->expandable_tables;
      $object->expandable_nodes = $all->expandable_nodes;
      // add curent table
      $object->tablename = $table;

      // For Tripal v2 compatibility
      // check if the current table maps to a node type-------------------------
      // If this table is connected to a node there will be a chado_tablename 
      // table in drupal.
      $base_tables = chado_get_base_tables();
      if (module_exists('tripal_core') and db_table_exists('chado_' . $table)) {
        // That has a foreign key to this one ($table_desc['primary key'][0]
        // and to the node table (nid).
        $sql = "
          SELECT $table_primary_key, nid
          FROM {chado_$table}
          WHERE $table_primary_key = :$table_primary_key
        ";
        $mapping = db_query($sql, [":$table_primary_key" => $object->{$table_primary_key}])->fetchObject();
        if ($mapping and $mapping->$table_primary_key) {
          $object->nid = $mapping->nid;
          $object->expandable_nodes[] = $table;
        }
      }

      // Check to see if the current record maps to an entity.  Because
      // multiple bundles can map to the same table we have to check
      // all bundles for this table.
      $entity_id = chado_get_record_entity_by_table($table, $object->{$table_primary_key});
      if ($entity_id) {
        $object->entity_id = $entity_id;
      }

      // Remove any fields where criteria needs to be evalulated----------------
      // The fields to be removed can be populated by implementing either
      // hook_exclude_field_from_<table>_by_default() where <table> is the 
      // current table OR hook_exclude_type_by_default() where there are fields 
      // of the specified type in the current table It only reaches this point 
      // if the criteria specified for whether or not to exclude the field 
      // includes <field_value> which means it has to be evaluated after
      // the query has been executed.
      foreach ($fields_to_remove as $field_name => $criteria) {

        // If the field is an object then we don't support exclusion of it
        // For example, if the field is a foreign key
        if (!isset($object->{$field_name})) {
          break;
        }

        // Replace <field_value> with the actual value of the field from the 
        // query.
        $field_name_safe = preg_replace('/\'|"|\\\/', '\\1', $object->{$field_name});
        $criteria = preg_replace('/<field_value>/', $field_name_safe, $criteria);

        // evaluate the criteria, if TRUE is returned then exclude the field
        // excluded fields can be expanded later by calling
        // chado_expand_var($var, 'field', <field name as shown in expandable_fields array>);
        $success = php_eval('<?php return ' . $criteria . '; ?>');
        if ($success) {
          unset($object->{$field_name});
          $object->expandable_fields[] = $table . '.' . $field_name;
        }
      }

      // Recursively follow foreign key relationships nesting objects as we go------------------------
      if (array_key_exists('foreign keys', $table_desc) and $table_desc['foreign keys']) {
        foreach ($table_desc['foreign keys'] as $foreign_key_array) {
          $foreign_table = $foreign_key_array['table'];
          foreach ($foreign_key_array['columns'] as $foreign_key => $primary_key) {

            // Note: Foreign key is the field in the current table whereas 
            // primary_key is the field in the table referenced by the foreign 
            // key, don't do anything if the foreign key is empty
            if (empty($object->{$foreign_key})) {
              continue;
            }

            if (is_array($include_fk)) {
              // Don't recurse if the callee has supplied an $fk_include list 
              // and this FK table is not in the list.
              if (is_array($include_fk) and !array_key_exists($foreign_key, $include_fk)) {
                $object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
                continue;
              }
            }
            // If we have the option but it is not an array then we don't 
            // recurse any further.
            if ($include_fk === TRUE) {
              $object->expandable_foreign_keys[] = $table . '.' . $foreign_key . ' => ' . $foreign_table;
              continue;
            }

            // Get the record from the foreign table.
            $foreign_values = [$primary_key => $object->{$foreign_key}];
            $options = [];
            if (is_array($include_fk)) {
              $options['include_fk'] = $include_fk[$foreign_key];
            }

            $foreign_object = chado_generate_var($foreign_table, $foreign_values, $options);

            // Add the foreign record to the current object in a nested manner.
            $object->{$foreign_key} = $foreign_object;
            // Flatten expandable_x arrays so only in the bottom object.
            if (property_exists($object->{$foreign_key}, 'expandable_fields') and
              is_array($object->{$foreign_key}->expandable_fields)) {
              $object->expandable_fields = array_merge(
                $object->expandable_fields,
                $object->{$foreign_key}->expandable_fields
              );
              unset($object->{$foreign_key}->expandable_fields);
            }
            if (property_exists($object->{$foreign_key}, 'expandable_foreign_keys') and
              is_array($object->{$foreign_key}->expandable_foreign_keys)) {
              $object->expandable_foreign_keys = array_merge(
                $object->expandable_foreign_keys,
                $object->{$foreign_key}->expandable_foreign_keys
              );
              unset($object->{$foreign_key}->expandable_foreign_keys);
            }
            if (property_exists($object->{$foreign_key}, 'expandable_tables') and
              is_array($object->{$foreign_key}->expandable_tables)) {
              $object->expandable_tables = array_merge(
                $object->expandable_tables,
                $object->{$foreign_key}->expandable_tables
              );
              unset($object->{$foreign_key}->expandable_tables);
            }
            if (property_exists($object->{$foreign_key}, 'expandable_nodes') and
              is_array($object->{$foreign_key}->expandable_nodes)) {
              $object->expandable_nodes = array_merge(
                $object->expandable_nodes,
                $object->{$foreign_key}->expandable_nodes
              );
              unset($object->{$foreign_key}->expandable_nodes);
            }
          }
        }
        $results[$key] = $object;
      }
    }
  }

  // Convert the results into an array.
  $results_arr = [];
  foreach ($results as $record) {
    $results_arr[] = $record;
  }
  // Check only one result returned.
  if (!$return_array) {
    if (sizeof($results_arr) == 1) {
      // Add results to object.
      return $results_arr[0];
    }
    elseif (!empty($results_arr)) {
      return $results_arr;
    }
    else {
      // No results returned.
    }
  }
  // The caller has requested results are always returned as
  // an array.
  else {
    if (!$results_arr) {
      return [];
    }
    else {
      return $results_arr;
    }
  }
}

/**
 * Retrieves fields, or tables that were excluded by default from a variable.
 *
 * The chado_generate_var() function automatically excludes some
 * fields and tables from the default form of a variable. Fields that are
 * extremely long, such as text fields are automatically excluded to prevent
 * long page loads.  Linking tables that have a many-to-one relationship with
 * the record are also excluded.  This function allows for custom expansion
 * of the record created by chado_generate_var() by specifyin the field and
 * tables that should be added.
 *
 * Example Usage:
 *
 * @code
 *  // Get a chado object to be expanded
 *  $values = array(
 *    'name' => 'Medtr4g030710'
 *  );
 *  $features = chado_generate_var('feature', $values);
 *  // Expand the feature.residues field
 *  $feature = chado_expand_var($feature, 'field', 'feature.residues');
 *  // Expand the feature properties (featureprop table)
 *  $feature = chado_expand_var($feature, 'table', 'featureprop');
 * @endcode
 *
 * If a field is requested, it's value is added where it normally is expected
 * in the record.  If a table is requested then a new key/value element is
 * added to the record. The key is the table's name and the value is an
 * array of records (of the same type created by chado_generate_var()). For
 * example, expanding a 'feature' record to include a 'pub' record via the
 * 'feature_pub' table.  The following provides a simple example for how
 * the 'feature_pub' table is added.
 *
 * @code
 * array(
 *   'feature_id' => 1
 *   'name' => 'blah',
 *   'uniquename' => 'blah',
 *   ....
 *   'feature_pub => array(
 *      [pub object],
 *      [pub object],
 *      [pub object],
 *      [pub object],
 *   )
 * )
 * @endcode
 *
 * where [pub object] is a record of a publication as created by
 * chado_generate_var().
 *
 * If the requested table has multiple foreign keys, such as the 'featureloc'
 * or 'feature_genotype' tables, then an additional level is added to the
 * array where the foreign key column names are added.  An example feature
 * record with an expanded featureloc table is shown below:
 *
 * @code
 * array(
 *   'feature_id' => 1
 *   'name' => 'blah',
 *   'uniquename' => 'blah',
 *   ....
 *   'featureloc => array(
 *      'srcfeature_id' => array(
 *        [feature object],
 *        ...
 *      )
 *      'feature_id' => array(
 *        [feature object],
 *        ...
 *      )
 *   )
 * )
 * @endcode
 *
 * @param $object
 *   This must be an object generated using chado_generate_var()
 * @param $type
 *   Indicates what is being expanded. Must be one of 'field', 'foreign_key',
 *   'table', 'node'. While field and node are self-explanitory, it might help
 *   to note that 'table' refers to tables that have a foreign key pointing to
 *   the current table (ie: featureprop is a table that can be expanded for
 *   features) and 'foreign_key' expands a foreign key in the current table
 *   that might have been excluded (ie: feature.type_id for features).
 * @param $to_expand
 *   The name of the field/foreign_key/table/node to be expanded
 * @param $table_options
 *   - order_by:
 *     An array containing options for the base table.  For example, an
 *     option of 'order_by' may be used to sort results in the base table
 *     if more than one are returned.  The options must be compatible with
 *     the options accepted by the chado_select_record() function.
 *   - return_array:
 *     Additionally,  The option 'return_array' can be provided to force
 *     the function to expand tables as an array. Default behavior is to expand
 *     a table as single record if only one record exists or to expand as an
 *     array if multiple records exist.
 *   - include_fk:
 *     an array of FK relationships to follow. By default, the
 *     chado_expand_var function will follow all FK relationships but this
 *     may generate more queries then is desired slowing down this function call
 *     when there are lots of FK relationships to follow.  Provide an array
 *     specifying the fields to include.  For example, if expanding a property
 *     table (e.g. featureprop) and you want the CV and accession but do not
 *     want the DB the following array would work:
 *        $table_options =  array(
 *          'include_fk' => array(
 *            'type_id' => array(
 *              'cv_id' => 1,
 *              'dbxref_id' => 1,
 *            )
 *          )
 *        );
 *
 *     The above array will expand the 'type_id' of the property table but only
 *     further expand the cv_id and the dbxref_id and will go no further.
 *   - pager:
 *     Use this option if it is desired to return only a subset of results
 *     so that they may be shown within a Drupal-style pager. This should be
 *     an array with two keys: 'limit' and 'element'.  The value of 'limit'
 *     should specify the number of records to return and 'element' is a
 *     unique integer to differentiate between pagers when more than one
 *     appear on a page.  The 'element' should start with zero and increment by
 *     one for each pager.  This only works when type is a 'table'.
 *   - filter:
 *     This options is only used where type=table and allows you to
 *     expand only a subset of results based on the given criteria. Criteria
 *     should provided as an array of [field name] => [value] similar to the
 *     values array provided to chado_generate_var(). For example, when
 *     expanding the featureprop table for a feature, you will already get only
 *     properties for that feature, this option allows you to further get only
 *     properties of a given type by passing in
 *     array('type_id' => array('name' => [name of type]))
 *
 * @return
 *   A chado object supplemented with the field/table/node requested to be
 *   expanded. If the type is a table and it has already been expanded no
 *   changes is made to the returned object
 *
 *
 * @ingroup tripal_chado_variables_api
 */
function chado_expand_var($object, $type, $to_expand, $table_options = []) {

  // Make sure we have a value.
  if (!$object) {
    $trace = (debug_backtrace(DEBUG_BACKTRACE_IGNORE_ARGS));
    tripal_report_error('tripal_chado',
      TRIPAL_ERROR,
      'Missing $object argument to the chado_expand_var function from %caller (line: %line)',
      ['%caller' => $trace[1]['function'], '%line' => $trace[0]['line']]);
    return $object;
  }

  // Check to see if we are expanding an array of objects.
  if (is_array($object)) {
    foreach ($object as $index => $o) {
      $object[$index] = chado_expand_var($o, $type, $to_expand);
    }
    return $object;
  }

  // Get the base table name.
  $base_table = $object->tablename;

  switch ($type) {
    case "field": //------------------------------------------------------------
      if (preg_match('/(\w+)\.(\w+)/', $to_expand, $matches)) {
        $tablename = $matches[1];
        $fieldname = $matches[2];
        $table_desc = chado_get_schema($tablename);

        // BASE CASE: the field is from the current table.
        if ($base_table == $tablename) {
          // Use the table description to fully describe the current object
          // in a $values array to be used to select the field from chado.
          $values = [];
          foreach ($table_desc['primary key'] as $key) {
            if (property_exists($object, $key)) {
              $values[$key] = $object->{$key};
            }
          }

          // Retrieve the field from Chado.
          $results = chado_select_record($tablename, [$fieldname], $values);

          // Check that the field was retrieved correctly.
          if (isset($results[0])) {
            $object->{$fieldname} = $results[0]->{$fieldname};
            $object->expanded = $to_expand;
          }
          // If it wasn't retrieved correctly, we need to warn the administrator.

        }
        // RECURSIVE CASE: the field is in a nested object.
        else {
          // We want to look at each field and if it's an object then we want to
          // attempt to expand the field in it via recursion.
          foreach ((array) $object as $field_name => $field_value) {
            if (is_object($field_value)) {
              $object->{$field_name} = chado_expand_var(
                $field_value,
                'field',
                $to_expand
              );
            }
          } // End of for each field in the current object.
        }
      }
      // Otherwise we weren't able to extract the parts of the field to expand
      // Thus we will warn the administrator.
      else {
        tripal_report_error('tripal_chado', TRIPAL_ERROR,
          'chado_expand_var: Field (%field) not in the right format. " .
          "It should be <tablename>.<fieldname>', ['%field' => $to_expand]);
      }
      break;

    case "foreign_key": //-----------------------------------------------------
      if (preg_match('/(\w+)\.(\w+) => (\w+)/', $to_expand, $matches)) {
        $table_name = $matches[1];
        $field_name = $matches[2];
        $foreign_table = $matches[3];
        $table_desc = chado_get_schema($table_name);

        // BASE CASE: The foreign key is from the current table.
        if ($base_table == $table_name) {

          // Get the value of the foreign key from the object
          $field_value = $object->{$field_name};

          // Get the name of the field in the foreign table using the table 
          // description For example, with the 
          // feature.type_id => cvterm.cvterm_id we need cvterm_id
          $foreign_field_name = FALSE;
          foreach ($table_desc['foreign keys'][$foreign_table]['columns'] as $left => $right) {
            if ($right == $field_name) {
              $foreign_field_name = $left;
            }
          }

          // Check that we were able to determine the field name in the foreign
          // table.
          if ($foreign_field_name) {

            // Generate a chado variable of the foreign key
            // For example, if the foreign key to expand is feature.type_id
            // then we want to generate a chado cvterm variable that matches the 
            // feature.type_id.
            $foreign_var = chado_generate_var(
              $foreign_table, // thus in the example above, generate a cvterm var
              [$foreign_field_name => $field_value], // where the cvterm.cvterm_id = feature.type_id value
              $table_options //pass in the same options given to this function
            );

            // Check that the foreign object was returned.
            if ($foreign_var) {

              // It was so now we can add this chado variable to our current 
              // object in place of the key value.
              $object->{$field_name} = $foreign_var;
              $object->expanded = $to_expand;

            }
            // Otherwise we weren't able to expand the foreign key
            else {
              tripal_report_error('tripal_chado', TRIPAL_ERROR,
                'chado_expand_var: unable to retrieve the object desribed by the foreign key
                while trying to expand %fk.',
                ['%fk' => $to_expand]);
            }
          }
          // Else we were unable to determine the field name in the foreign table.
          else {
            tripal_report_error('tripal_chado', TRIPAL_ERROR,
              'chado_expand_var: unable to determine the field name in the table the foreign
              key points to while trying to expand %fk.',
              ['%fk' => $to_expand]);
          }

        }
        // RECURSIVE CASE: Check any nested objects.
        else {

          foreach ((array) $object as $field_name => $field_value) {
            if (is_object($field_value)) {
              $object->{$field_name} = chado_expand_var(
                $field_value,
                'foreign_key',
                $to_expand
              );
            }
          } //End of for each field in the current object.

        }
      }
      // Otherwise we weren't able to extract the parts of the foreign key to 
      // expand thus we will warn the administrator.
      else {
        tripal_report_error('tripal_chado', TRIPAL_ERROR,
          'chado_expand_var: foreign_key (%fk) not in the right format. " .
          "It should be <tablename>.<fieldname>', ['%fk' => $to_expand]);
      }
      break;

    case "table": //------------------------------------------------------------
      $foreign_table = $to_expand;

      // BASE CASE: don't expand the table it already is expanded
      if (property_exists($object, $foreign_table)) {
        return $object;
      }
      $foreign_table_desc = chado_get_schema($foreign_table);

      // If we don't get a foreign_table (which could happen of a custom 
      // table is not correctly defined or the table name is mispelled then we 
      // should return gracefully.
      if (!is_array($foreign_table_desc)) {
        return $object;
      }

      // BASE CASE: If it's connected to the base table via a FK constraint
      // then we have all the information needed to expand it now.
      if (array_key_exists($base_table, $foreign_table_desc['foreign keys'])) {
        foreach ($foreign_table_desc['foreign keys'][$base_table]['columns'] as $left => $right) {
          // if the FK value in the base table is not there then we can't expand
          // it, so just skip it.
          if (!$object->{$right}) {
            continue;
          }

          // If the user wants to limit the results they expand, make sure
          // those criteria are taken into account.
          if (isset($table_options['filter'])) {
            if (is_array($table_options['filter'])) {
              $filter_criteria = $table_options['filter'];
              $filter_criteria[$left] = $object->{$right};
            }
            else {

              // If they supplied criteria but it's not in the correct format
              // then warn them but proceed as though criteria was not supplied.
              $filter_criteria = [$left => $object->{$right}];

              tripal_report_error('tripal_chado', TRIPAL_WARNING,
                'chado_expand_var: unable to apply supplied filter criteria
                since it should be an array. You supplied %criteria',
                ['%criteria' => print_r($table_options['filter'], TRUE)]
              );
            }
          }
          else {
            $filter_criteria = [$left => $object->{$right}];
          }

          // Generate a new object for this table using the FK values in the 
          // base table.
          $new_options = $table_options;
          $foreign_object = chado_generate_var($foreign_table, $filter_criteria, $new_options);

          // If the generation of the object was successful, update the base 
          // object to include it.
          if ($foreign_object) {
            // In the case where the foreign key relationship exists more
            // than once with the same table we want to alter the array 
            // structure to include the field name.
            if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
              if (!property_exists($object, $foreign_table)) {
                $object->{$foreign_table} = new stdClass();
              }
              $object->{$foreign_table}->{$left} = $foreign_object;
              $object->expanded = $to_expand;

            }
            else {
              if (!property_exists($object, $foreign_table)) {
                $object->{$foreign_table} = new stdClass();
              }
              $object->{$foreign_table} = $foreign_object;
              $object->expanded = $to_expand;
            }
          }
          // If the object returned is NULL then handle that.
          else {
            // In the case where the foreign key relationship exists more
            // than once with the same table we want to alter the array 
            // structure to include the field name.
            if (count($foreign_table_desc['foreign keys'][$base_table]['columns']) > 1) {
              if (!property_exists($object, $foreign_table)) {
                $object->{$foreign_table} = new stdClass();
              }
              $object->{$foreign_table}->{$left} = NULL;
            }
            else {
              $object->{$foreign_table} = NULL;
            }
          }
        }
      }
      // RECURSIVE CASE: if the table is not connected directly to the current 
      // base table through a foreign key relationship, then maybe it has a 
      // relationship to one of the nested objects.
      else {

        // We need to recurse -the table has a relationship to one of the nested
        // objects. We assume it's a nested object if the value of the field is 
        // an object.
        $did_expansion = 0;
        foreach ((array) $object as $field_name => $field_value) {

          // CASE #1: This field is an already expanded foreign key and the 
          // table to be expanded is in the table referenced by the foreign key.

          // First of all it can only be expanded if it's an object
          // And if it's a foreign key it should have a tablename property.
          if (is_object($field_value) AND property_exists($field_value, 'tablename')) {
            $object->{$field_name} = chado_expand_var($field_value, 'table', $foreign_table);
          }

          // CASE #2: This field is an already expanded object (ie: the field is
          // actually the expanded table name) and the table to be expanded is 
          // related to it.

          // Check to see if the $field_name is a valid chado table, we don't 
          // need to call chado_expand_var on fields that aren't tables.
          $check = chado_get_schema($field_name);
          if ($check) {
            $did_expansion = 1;
            $object->{$field_name} = chado_expand_var($field_value, 'table', $foreign_table);
          }
        }

        // If we did not expand this table we should return a message that the 
        // foreign tabl could not be expanded.
        if (!$did_expansion) {
          tripal_report_error('tripal_chado', TRIPAL_ERROR, 'chado_expand_var: Could not expand %table. ' .
            'The table is either not related to the base object through a foreign key relationships or ' .
            'it is already expanded. First check the object to ensure it doesn’t already contain the ' .
            'data needed and otherwise check the table definition using chado_get_schema() to ensure ' .
            'a proper foreign key relationship is present.',
            ['%table' => $foreign_table]);
        }
      }
      break;

    case "node": //-------------------------------------------------------------

      // BASE CASE: if the node to be expanded is for our base table, then just 
      // expand it.
      if ($object->tablename == $to_expand) {

        // Load the node based on the current objects nid (node primary key).
        $node = NULL;
        if (property_exists($object, 'nid')) {
          $node = node_load($object->nid);
        }
        // Try to get the nid based on the tablename.
        else {
          // Invoke all hook_node_info to avoid hard-coding the chado_$table 
          // assumption..
          foreach (module_invoke_all('node_info') as $node_info) {
            if (array_key_exists('chado_node_api', $node_info)) {
              if ($node_info['chado_node_api']['base_table'] == $object->tablename) {
                $key_name = $node_info['chado_node_api']['base_table'] . '_id';
                $nid = chado_get_nid_from_id(
                  $node_info['chado_node_api']['base_table'],
                  $object->{$key_name},
                  $node_info['base']);
                if ($nid > 0) {
                  $object->nid = $nid;
                  $node = node_load($nid);
                  break;
                }
              }
            }
          }
        }

        // If we have successfully loaded the node...
        if ($node) {

          // Move expandable arrays from the object into the node.
          $object->expanded = $to_expand;
          $node->expandable_fields = $object->expandable_fields;
          unset($object->expandable_fields);
          $node->expandable_tables = $object->expandable_tables;
          unset($object->expandable_tables);
          $node->expandable_nodes = $object->expandable_nodes;
          unset($object->expandable_nodes);

          // The node becomes the base object with the obejct added to it.
          // For example, we may start with a feature object with a name, 
          // uniquename , type, etc. After expanding we will return the node and
          // at $node->feature you will find the original object.
          $node->{$base_table} = $object;
          $object = $node;

        }
        // Else we were unable to load the node.
        else {

          // Warn the administrator
          if (isset($object->nid)) {
            tripal_report_error('tripal_chado', TRIPAL_ERROR, 'chado_expand_var: No node matches the nid (%nid) supplied.',
              ['%nid' => $object->nid]);
          }
          else {
            tripal_report_error('tripal_chado', TRIPAL_NOTICE, 'chado_expand_var: There is no node for the current object: <pre>%object</pre>', ['%object' => print_r($object, TRUE)]);
          }
        } //End of if node.
      }
      // RECURSIVE CASE: check to see if the node to be expanded associates with 
      // a chado table within one of the nested objects.
      else {

        // We need to recurse -the node to expand is one of the nested objects
        // We assume it's a nested object if the field value is an object.
        foreach ((array) $object as $field_name => $field_value) {
          if (is_object($field_value)) {
            $object->{$field_name} = chado_expand_var(
              $field_value,
              'node',
              $to_expand
            );
          }
        } // End of for each field in the current object.
      }
      break;

    // The $type to be expanded is not yet supported.
    default:
      tripal_report_error('tripal_chado', TRIPAL_ERROR, 'chado_expand_var: Unrecognized type (%type). Should be one of "field", "table", "node".',
        ['%type' => $type]);
      return FALSE;
  }

  // Move expandable arrays downwards -------------------------------
  // If the type was either table or foreign key then a new chado variable was 
  // generated this variable will have it's own expandable array's which need to
  // be moved down and merged with the base objects expandable arrays.

  // Thus, check all nested objects for expandable arrays
  // and if they have them, move them downwards.
  foreach ((array) $object as $field_name => $field_value) {
    if (is_object($field_value)) {

      // The current nested object has expandable arrays.
      if (isset($field_value->expandable_fields)) {

        // Move expandable fields downwards.
        if (isset($field_value->expandable_fields) and is_array($field_value->expandable_fields)) {

          // If the current object has it's own expandable fields then merge them.
          if (isset($object->expandable_fields)) {
            $object->expandable_fields = array_merge(
              $object->expandable_fields,
              $object->{$field_name}->expandable_fields
            );
            unset($object->{$field_name}->expandable_fields);

          }
          // Otherwise, just move the expandable fields downwards.
          else {
            $object->expandable_fields = $object->{$field_name}->expandable_fields;
            unset($object->{$field_name}->expandable_fields);
          }

        }

        // Move expandable foreign keys downwards.
        if (isset($field_value->expandable_foreign_keys) and is_array($field_value->expandable_foreign_keys)) {

          // If the current object has it's own expandable foreign keys then 
          // merge them.
          if (isset($object->expandable_foreign_keys)) {
            $object->expandable_foreign_keys = array_merge(
              $object->expandable_foreign_keys,
              $object->{$field_name}->expandable_foreign_keys
            );
            unset($object->{$field_name}->expandable_foreign_keys);

          }
          // Otherwise, just move the expandable foreign keys downwards.
          else {
            $object->expandable_foreign_keys = $object->{$field_name}->expandable_foreign_keys;
            unset($object->{$field_name}->expandable_foreign_keys);
          }
        }

        // Move expandable tables downwards.
        if (isset($field_value->expandable_tables) and is_array($field_value->expandable_tables)) {

          // If the current object has it's own expandable tables then merge them.
          if (isset($object->expandable_tables)) {
            $object->expandable_tables = array_merge(
              $object->expandable_tables,
              $object->{$field_name}->expandable_tables
            );
            unset($object->{$field_name}->expandable_tables);

          }
          // Otherwise, just move the expandable tables downwards.
          else {
            $object->expandable_tables = $object->{$field_name}->expandable_tables;
            unset($object->{$field_name}->expandable_tables);
          }
        }

        // Move expandable nodes downwards.
        if (isset($field_value->expandable_nodes) and is_array($field_value->expandable_nodes)) {

          // If the current object has it's own expandable tables then merge them.
          if (isset($object->expandable_nodes)) {
            $object->expandable_nodes = array_merge(
              $object->expandable_nodes,
              $object->{$field_name}->expandable_nodes
            );
            unset($object->{$field_name}->expandable_nodes);

          }
          // Otherwise, just move the expandable tables downwards.
          else {
            $object->expandable_nodes = $object->{$field_name}->expandable_nodes;
            unset($object->{$field_name}->expandable_nodes);
          }
        }
      }
    }
  }

  // Move extended array downwards ----------------------------------
  // This tells us what we have expanded (ie: that we succeeded)
  // and is needed to remove the entry from the expandable array.

  // If there is no expanded field in the current object then check any of the 
  // nested objects and move it down.
  if (!property_exists($object, 'expanded')) {

    // It's a nested object if the value is an object.
    foreach ((array) $object as $field_name => $field_value) {
      if (is_object($field_value)) {

        // Check if the current nested object has an expanded array.
        if (isset($field_value->expanded)) {

          // If so, then move it downwards.
          $object->expanded = $field_value->expanded;
          unset($field_value->expanded);
        }
      }
    }
  }

  // Check again if there is an expanded field in the current object
  // We check again because it might have been moved downwards above.
  if (property_exists($object, 'expanded')) {

    // If so, then remove the expanded identifier from the correct expandable 
    // array..
    $expandable_name = 'expandable_' . $type . 's';
    if (property_exists($object, $expandable_name) and $object->{$expandable_name}) {
      $key_to_remove = array_search($object->expanded, $object->{$expandable_name});
      unset($object->{$expandable_name}[$key_to_remove]);
      unset($object->expanded);

    }
  }

  // Finally, Return the object!
  return $object;
}