tripal/tripal_core/api/tripal_core.chado_variables.api.inc

<?php
/**
 * @file
 * This API generates objects containing the full details of a record(s) in chado.
 */

/**
 * Implements hook_exclude_type_by_default()
 *
 * This hooks allows fields of a specified type that match a specified criteria to be excluded by
 * default from any table when chado_generate_var() is called. Keep in mind that if
 * fields are excluded by default they can always be expanded at a later date using
 * chado_expand_var().
 *
 * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
 * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
 * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
 * contain the following tokens:
 *   - &gt;field_name&lt;
 *       Replaced by the name of the field to be excluded
 *   - &gt;field_value&lt;
 *       Replaced by the value of the field in the current record
 * Also keep in mind that if your criteria doesn't contain the &gt;field_value&lt;  token then it will be
 * evaluated before the query is executed and if the field is excluded it won't be included in the
 * query.
 *
 * @return
 *   An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
 *
 * @ingroup tripal_chado_query_api
 */
function tripal_core_exclude_type_by_default() {
  return array('text' => 'strlen("&gt;field_value&lt; ") > 100');
}

/**
 * Implements hook_exclude_field_from_<tablename>_by_default()
 *
 * This hooks allows fields from a specified table that match a specified criteria to be excluded by
 * default from any table when chado_generate_var() is called. Keep in mind that if
 * fields are excluded by default they can always be expanded at a later date using
 * chado_expand_var().
 *
 * Criteria are php strings that evaluate to either TRUE or FALSE. These strings are evaluated using
 * drupal_eval() which suppresses syntax errors and throws watchdog entries of type php. There are
 * also watchdog entries of type tripal_core stating the exact criteria evaluated. Criteria can
 * contain the following tokens:
 *   - &gt;field_name&lt;
 *       Replaced by the name of the field to be excluded
 *   - &gt;field_value&lt;
 *       Replaced by the value of the field in the current record
 * Also keep in mind that if your criteria doesn't contain the &gt;field_value&lt;  token then it will be
 * evaluated before the query is executed and if the field is excluded it won't be included in the
 * query.
 *
 * @return
 *   An array of type => criteria where the type is excluded if the criteria evaluates to TRUE
 *
 * @ingroup tripal_chado_query_api
 */
function tripal_core_exclude_field_from_feature_by_default() {
  return array();
}

/**
 * Generates an array containing the full details of a record(s) in chado. The 
 * returned array differs from the array returned by chado_select_record as all foreign key
 * relationships have been followed and those data are also included. The array
 * returned by this function can be used with chado_expand_var function to add
 * additional FK relationships that were not included because they were not
 * a one-to-one mapping or for fields that were excluded such as large text fields.
 *  
 *
 * @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.  This only works when type is a 'table'.
 * @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.
 *
 * Example Usage:
 * @code
   $values = array(
     'name' => 'Medtr4g030710'
   );
   $features = chado_generate_var('feature', $values);
 * @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. For example:
 * @code
   mymodule_exclude_field_from_feature_by_default() {
     return array('residues' => TRUE);
   }
 * @endcode
 *      will ensure that feature.residues is ecluded from a feature object by default.
 *  - hook_exclude_type_by_default:
 *      This hook allows you to exclude fields from all tables that are of a given postgresql field
 *      type. Simply implement this hook to return an array of postgresql types mapped to criteria.
 *      Then all fields of that type where the criteria supplied returns TRUE will be excluded from
 *      any table. Tokens available in criteria are &gt;field_value&lt;  and &gt;field_name&lt; . For example:
 * @code
   mymodule_exclude_type_by_default() {
     return array('text' => 'length(&gt;field_value&lt; ) > 50');
   }
 * @endcode
 *      will exclude all text fields with a length > 50. Thus if $feature.residues is longer than 50 *      it will be excluded, otherwise it will be added.
 *
 * @ingroup tripal_chado_query_api
 */
function chado_generate_var($table, $values, $base_options = array()) {
  $all = new stdClass();

  $return_array = 0;
  if (array_key_exists('return_array', $base_options)) {
    $return_array = 1;
  }
  $include_fk = 0;
  if (array_key_exists('include_fk', $base_options)) {
    $include_fk = $base_options['include_fk'];
  }
  $pager = array();
  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_core', 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.", array('%table' => $table));
    if ($return_array) {
      return array();
    }
    return FALSE;
  }
  $table_primary_key = $table_desc['primary key'][0];
  $table_columns = array_keys($table_desc['fields']);

  // Expandable fields without value needed for criteria--------------------------------------------
  $all->expandable_fields = array();
  if (array_key_exists('referring_tables', $table_desc) and $table_desc['referring_tables']) {
    $all->expandable_tables = $table_desc['referring_tables'];
  }
  else {
    $all->expandable_tables = array();
  }
  $all->expandable_nodes = array();

  /*
  // Get fields to be removed by name.................................
  $fields_to_remove = module_invoke_all('exclude_field_from_' . $table . '_by_default');
  foreach ($fields_to_remove as $field_name => $criteria) {
    //replace &gt;field_name&lt;  with the current field name &
    $criteria = preg_replace('/&gt;field_name&lt; /', addslashes($field_name), $criteria);
    // if field_value needed we can't deal with this field yet
    if (preg_match('/&gt;field_value&lt; /', $criteria)) {
      break;
    }

    //if criteria then remove from query
    // @coder-ignore: only module designers can populate $criteria -not 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................................
  $types_to_remove = module_invoke_all('exclude_type_by_default');
  $field_types = array();
  foreach ($table_desc['fields'] as $field_name => $field_array) {
    $field_types[$field_array['type']][] = $field_name;
  }
  foreach ($types_to_remove as $field_type => $criteria) {
    // if there are fields of that type to remove
    if (is_array($field_types[$field_type])) {
      //replace &gt;field_name&lt;  with the current field name &
      $criteria = preg_replace('/&gt;field_name&lt; /', addslashes($field_name), $criteria);
      foreach ($field_types[$field_type] as $field_name) {
        // if field_value needed we can't deal with this field yet
        if (preg_match('/&gt;field_value&lt; /', $criteria)) {
          $fields_to_remove[$field_name] = $criteria;
          continue;
        }
        // if field_value needed we can't deal with this field yet
        if (preg_match('/&gt;field_value&lt; /', $criteria)) {
          break;
        }
        //if criteria then remove from query
        // @coder-ignore: only module designers can populate $criteria -not 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 ($results) {
    foreach ($results as $key => $object) {
      // Add empty expandable_x arrays
      $object->expandable_fields = $all->expandable_fields;
      $object->expandable_tables = $all->expandable_tables;
      $object->expandable_nodes = $all->expandable_nodes;
      // add curent table
      $object->tablename = $table;

      // 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
      if (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, array(":$table_primary_key" => $object->{$table_primary_key}))->fetchObject();
        if ($mapping and $mapping->$table_primary_key) {
          $object->nid = $mapping->nid;
          $object->expandable_nodes[] = $table;
        }
      }

      // remove any fields where criteria needs to be evalulated---------------------------------------
/*      foreach ($fields_to_remove as $field_name => $criteria) {
        if (!isset($object->{$field_name})) {
          break;
        }
        $criteria = preg_replace('/&gt;field_value&lt; /', addslashes($object->{$field_name}), $criteria);
        $success = php_eval('<?php return ' . $criteria . '; ?>');
        if ($success) {
          unset($object->{$field_name});
          $object->expandable_fields[] = $table . '.' . $field_name;
        }
      }
*/
      // recursively follow foreign key relationships nesting objects as we go------------------------
      if ($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 => $primary_key) {
            // Note: Foreign key is the field in the current table whereas primary_key is the field in
            // the table referenced by the foreign key
            //Dont do anything if the foreign key is empty
            if (empty($object->{$foreign_key})) {
              continue;
            }

            if ($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, $include_fk)) {
                continue;
              }
              // if we have the option but it is not an array then we don't recurse any furutehr
              if (!is_array($include_fk)) {
                continue;
              }
            }
            // get the record from the foreign table
            $foreign_values = array($primary_key => $object->{$foreign_key});
            $options = array();
            if (is_array($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_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
  $results_arr = array();
  foreach ($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 array();
    }
    else {
      return $results_arr;
    }
  }
}

/**
 * Retrieves fields/tables/nodes that were excluded by default from a variable and adds them
 *
 * This function exists to allow chado_generate_var() to excldue some
 * fields/tables/nodes from the default form of a variable without making it extremely difficult for
 * the tripal admin to get at these variables if he/she wants them.
 *
 * @param $object
 *   This must be an object generated using chado_generate_var()
 * @param $type
 *   Must be one of 'field', 'table', 'node'. Indicates what is being expanded.
 * @param $to_expand
 *   The name of the field/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'.
 * @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
 *
 * Example Usage:
 * @code
   // Get a chado object to be expanded
   $values = array(
     'name' => 'Medtr4g030710'
   );
   $features = chado_generate_var('feature', $values);
   // Expand the organism node
   $feature = chado_expand_var($feature, 'node', 'organism');
   // 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
 *
 * @ingroup tripal_chado_query_api
 */
function chado_expand_var($object, $type, $to_expand, $table_options = array()) {

  // make sure we have a value
  if (!$object) {
    tripal_report_error('tripal_core', TRIPAL_ERROR,
      'Cannot pass non array as argument, $object, to chado_expand_var function.', array());
    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);
        $values = array();
        foreach ($table_desc['primary key'] as $key) {
          if(property_exists($object, $key)) {
            $values[$key] = $object->{$key};
          }
        }
        if ($base_table == $tablename) {
          //get the field
          $results = chado_select_record($tablename, array($fieldname), $values);
          $object->{$fieldname} = $results[0]->{$fieldname};
          $object->expanded = $to_expand;
        }
        else {
          //We need to recurse -the field is in a nested object
          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
        }
      }
      else {
        tripal_report_error('tripal_core', TRIPAL_ERROR,
          'chado_expand_var: Field (%field) not in the right format. " .
          "It should be <tablename>.<fieldname>');
      }
      break;
    case "table": //--------------------------------------------------------------------------------
      $foreign_table = $to_expand;

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

      // If it's connected to the base table via a FK constraint
      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;
          }

          // 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, array($left => $object->{$right}), $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;
            }
          }
        }
      }
      // if the foreign table is not connected to the base table through a FK constraint
      else {
        // We need to recurse -the table has a relationship to one of the nested objects
        $did_expansion = 0;
        foreach ((array) $object as $field_name => $field_value) {
          // if we have a nested object ->expand the table in 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', $foreign_table);
          }
        }
        // if we did not expand this table we should return a message that the foreign table
        // could not be expanded
        if (!$did_expansion) {
          tripal_report_error('tripal_core', TRIPAL_ERROR, 'chado_expand_var: Could not expand table, %table. It is ' .
            'not in a foreign key relationship with the base object nor with any other expanded table. ' .
            'Check the table definition to ensure that a proper foreign key relationship is present.',
            array('%table' => $foreign_table));
        }
      }
      break;
    case "node": //---------------------------------------------------------------------------------
      //if the node to be expanded is for our base table, then just expand it
      if ($object->tablename == $to_expand) {
        $node = node_load($object->nid);
        if ($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);
          $node->{$base_table} = $object;
          $object = $node;
        }
        else {
          tripal_report_error('tripal_core', TRIPAL_ERROR, 'chado_expand_var: No node matches the nid (%nid) supplied.',
            array('%nid' => $object->nid));
        } //end of if node
      }
      else {
        //We need to recurse -the node to expand is one of the nested objects
        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;
    default:
      tripal_report_error('tripal_core', TRIPAL_ERROR, 'chado_expand_var: Unrecognized type (%type). Should be one of "field", "table", "node".',
        array('%type' => $type));
      return FALSE;
  }

  // move extended array downwards
  if (!property_exists($object, 'expanded')) {
    //if there's no extended field then go hunting for it
    foreach ( (array)$object as $field_name => $field_value) {
      if (is_object($field_value)) {
        if (isset($field_value->expanded)) {
          $object->expanded = $field_value->expanded;
          unset($field_value->expanded);
        }
      }
    }
  }
  //try again becasue now we might have moved it down
  if (property_exists($object, 'expanded')) {
    $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);
    }
    else {
      // if there is an expandable array then we've reached the base object
      // if we get here and don't have anything expanded then something went wrong
      //      tripal_report_error('tripal_core', TRIPAL_ERROR,
      //        'chado_expand_var: Unable to expand the %type %to_expand',
      //        array('%type'=>$type, '%to_expand'=>$to_expand),
      //      );
    } //end of it we've reached the base object
  }

  return $object;
}