tripal/tripal_analysis/api/tripal_analysis.api.inc

<?php
/**
 * @file
 * Provides functions for managing analysis'.
 *
 * @ingroup tripal_analysis
 */

/**
 * @defgroup tripal_analysis_api Analysis Module API
 * @ingroup tripal_api
 * @{
 * Provides an interface for specialized analysis modules to extend the basic functionality.
 * @}
 */

/**
 * Register tripal_analysis_api sub-modules
 *
 * @param $modulename
 *  The name of the module to be registered as a tripal analysis submodule
 *
 * @ingroup tripal_analysis_api
 */
function tripal_analysis_api_register_child($modulename) {
  $sql = "SELECT * FROM {tripal_analysis_api} WHERE modulename = :modname";
  if (!db_query($sql, array(':modname' => $modulename))->fetchField()) {
    $sql = "INSERT INTO {tripal_analysis_api} (modulename) VALUES (:modname)";
    db_query($sql, array(':modname' => $modulename));
  }
}

/**
 * Un-register a tripal analysis sub-module
 *
 * @param $modulename
 *  The name of the module to un-register
 *
 * @ingroup tripal_analysis_api
 */
function tripal_analysis_api_unregister_child($modulename) {
  if (db_table_exists('tripal_analysis_api')) {
      $sql = "DELETE FROM {tripal_analysis_api} WHERE modulename = :modname";
      db_query($sql, array(':modname' => $modulename));
  }
}

/**
 * Retrieve properties of a given type for a given analysis
 *
 * @param $analysis_id
 *    The analysis_id of the properties you would like to retrieve
 * @param $property
 *    The cvterm name of the properties to retrieve
 * @param $cvname
 *   The name of the vocabulary to which the term belongs. Defaults to 'tripal'.
 *
 * @return
 *    An analysis chado variable with the specified properties expanded
 *
 * @ingroup tripal_analysis_api
 */
function tripal_analysis_api_get_property($analysis_id, $property, $cvname = 'tripal') {
  return chado_get_property('analysis', $analysis_id, $property, $cvname);
}

/**
 * Insert a given property
 *
 * @param $analysis_id
 *   The analysis_id of the property to insert
 * @param $property
 *   The cvterm name of the property to insert
 * @param $value
 *   The value of the property to insert
 * @param $update_if_present
 *   A boolean indicated whether to update the record if it's already present
 * @param $cvname
 *   The name of the vocabulary to which the term belongs. Defaults to 'tripal'.
 *
 * @return
 *   True of success, False otherwise
 *
 * @ingroup tripal_analysis_api
 */
function tripal_analysis_api_insert_property($analysis_id, $property, $value, $update_if_present = 0, $cvname = 'tripal') {
    return chado_insert_property('analysis', $analysis_id, $property, $cvname, $value, $update_if_present);
}

/**
 * Update a given property
 *
 * @param $analysis_id
 *   The analysis_id of the property to update
 * @param $property
 *   The cvterm name of the property to update
 * @param $value
 *   The value of the property to update
 * @param $insert_if_missing
 *   A boolean indicated whether to insert the record if it's absent
 * @param $cvname
 *   The name of the vocabulary to which the term belongs. Defaults to 'tripal'.
 *
 * Note: The property will be identified using the unique combination of the $analysis_id and $property
 * and then it will be updated with the supplied value
 *
 * @return
 *   True of success, False otherwise
 *
 * @ingroup tripal_analysis_api
 */
function tripal_analysis_api_update_property($analysis_id, $property, $value, $insert_if_missing = 0, $cvname = 'tripal') {
  return chado_update_property('analysis', $analysis_id, $property, $cvname, $value, $insert_if_missing);
}

/**
 * Delete a given property
 *
 * @param $analysis_id
 *   The analysis_id of the property to delete
 * @param $property
 *   The cvterm name of the property to delete
 * @param $cvname
 *   The name of the vocabulary to which the term belongs. Defaults to 'tripal'.
 *
 * Note: The property will be identified using the unique combination of the $analysis_id and $property
 * and then it will be deleted
 *
 * @return
 *   True of success, False otherwise
 *
 * @ingroup tripal_analysis_api
 */
function tripal_analysis_api_delete_property($analysis_id, $property, $cvname = 'tripal') {
  return chado_delete_property('analysis', $analysis_id, $property, $cvname);
}

/**
 * Retreives the node of a sync'ed analysis
 *
 * @param $analysis_id
 *   The analysis_id of the property to delete
 *
 * @return
 *   node of analysis on success, null otherwise
 *
 * @ingroup tripal_analysis_api
 */
function tripal_analysis_api_get_node($analysis_id) {
  $sql = "SELECT *
           FROM {chado_analysis} CA
              INNER JOIN {node} N on CA.nid = N.nid
           WHERE analysis_id = :analysis_id";
  $node = db_query($sql, array(':analysis_id' => $analysis_id))->fetchObject();
  return $node;
}