'feature_property' ); $cv_object = tripal_cv_get_cv($select_values); * @endcode * The above code selects the feature_property cv and returns the following object: * @code $cv_object = stdClass Object ( [cv_id] => 13 [name] => feature_property [definition] => ); * @endcode * * @ingroup tripal_cv_api */ function tripal_cv_get_cv ($select_values) { /** $columns = array( 'cv_id', 'name', 'definition', ); $results = tripal_core_chado_select('cv', $columns, $select_values); if (sizeof($results) == 1) { return $results[0]; } elseif (empty($results)) { watchdog('tripal_cv', 'tripal_cv_get_cv: No cv matches criteria values:%values', array('%values' => print_r($select_values, TRUE)), WATCHDOG_WARNING ); return FALSE; } else { watchdog('tripal_cv', 'tripal_cv_get_cv: 2+ cvs match criteria values:%values', array('%values' => print_r($select_values, TRUE)), WATCHDOG_WARNING ); } */ } // Purpose: To retrieve a chado cv object // @param $where_options // @code // array( // => array( // 'type' => , // 'value' => , // 'exact' => , // ) // ) // @endcode // // @return // Chado cv object with all fields from the chado cv table // // @ingroup tripal_cv_api // //function tripal_cv_get_cv ($where_options) /** * * * @param $name * The name of the cv to be returned * @return * The cv object for the specified CV name * * @ingroup tripal_cv_api */ function tripal_cv_get_cv_by_name ($name) { $previous_db = tripal_db_set_active('chado'); $r = db_fetch_object(db_query("SELECT * FROM cv WHERE name = '%s'",$name)); tripal_db_set_active($previous_db); return $r; } /** * return the cv object for the specified CV id * * @ingroup tripal_cv_api */ function tripal_cv_get_cv_by_id ($cv_id) { $previous_db = tripal_db_set_active('chado'); $r = db_fetch_object(db_query("SELECT * FROM cv WHERE cv_id = %d",$cv_id)); tripal_db_set_active($previous_db); return $r; } /** * Purpose: Create an options array to be used in a form element * which provides a list of all chado cvs * * @return * An array(cv_id => name) for each cv in the chado cv table * * @ingroup tripal_cv_api */ function tripal_cv_get_cv_options() { $previous_db = tripal_db_set_active('chado'); $result = db_query( "SELECT cv_id, name FROM cv" ); tripal_db_set_active($previous_db); $options = array(); while ( $r = db_fetch_object($result) ) { $options[$r->cv_id] = $r->name; } return $options; } /** * Purpose: To retrieve a chado controlled vocabulary term object * * @param $select_values * An array meant to uniquely select a given controlled vocabulary term * * @return * Chado controlled vocabulary term object * * The controlled vocabulary term is selected using tripal_core_chado select and as such the * $select_values array parameter meant to uniquely identify the controlled vocab term to be * returned follows the same form as when using tripal_core_chado_select directly. * * Example Usage: * @code $select_values = array( 'name' => 'synonym', 'cv_id' => array( 'name' => 'feature_property' ) ); $cvterm_object = tripal_cv_get_cvterm($select_values); * @endcode * The above code selects the synonym cvterm from the feature_proeprty cv and returns * the following object: * @code $cvterm_object = stdClass Object ( [cvterm_id] => 2099 [name] => synonym [definition] => Historic community symbol, may have originally been symbol [] [is_obsolete] => 0 [is_relationshiptype] => 1 [cv_cv_id] => 13 [cv_name] => feature_property [cv_definition] => [dbreference_dbxref_id] => 2581 [dbreference_accession] => synonym [dbreference_description] => [dbreference_version] => [dbreference_db_db_id] => 49 [dbreference_db_name] => SOFP [dbreference_db_description] => [dbreference_db_urlprefix] => [dbreference_db_url] => ); * @endcode * * @ingroup tripal_cv_api */ function tripal_cv_get_cvterm ($select_values) { /** $columns = array( 'cvterm_id', 'cv_id', 'name', 'definition', 'dbxref_id', 'is_obsolete', 'is_relationshiptype' ); $results = tripal_core_chado_select('cvterm', $columns, $select_values); if (sizeof($results) == 1) { // Add cv $cvterm = tripal_cv_add_cv_to_object(array('cv_id'=>$results[0]->cv_id),$results[0],array()); unset($cvterm->cv_id); // Add dbxref $cvterm = tripal_db_add_dbxref_to_object(array('dbxref_id'=>$cvterm->dbxref_id),$cvterm,array()); unset($cvterm->dbxref_id); return $cvterm; } elseif (empty($results)) { watchdog('tripal_cv', 'tripal_cv_get_cvterm: No cvterm matches criteria values:%values', array('%values' => print_r($select_values, TRUE)), WATCHDOG_WARNING ); return FALSE; } else { watchdog('tripal_cv', 'tripal_cv_get_cvterm: 2+ cvterms match criteria values:%values', array('%values' => print_r($select_values, TRUE)), WATCHDOG_WARNING ); } */ } /** * Purpose: Retrieve a chado cvterm object with a given name * * @param $name * the cvterm.name * @param $cv_id * the cv_id of the term you are looking for * * @return * cvterm object * * @ingroup tripal_cv_api */ function tripal_cv_get_cvterm_by_name ($name, $cv_id=0) { if (!empty($cv_id)) { $sql = "SELECT * FROM cvterm WHERE name='%s' AND cv_id=%d"; $previous_db = tripal_db_set_active('chado'); $r = db_fetch_object(db_query($sql, $name, $cv_id)); tripal_db_set_active($previous_db); } else { $sql = "SELECT * FROM cvterm WHERE name='%s'"; $previous_db = tripal_db_set_active('chado'); $r = db_fetch_object(db_query($sql, $name)); tripal_db_set_active($previous_db); } return $r; } /** * Purpose: Create an options array to be used in a form element * which provides a list of all chado cvterms * * @param $cv_id * The chado cv_id; * only cvterms with the supplied cv_id will be returned * @return * An array(cvterm_id => name) * for each cvterm in the chado cvterm table where cv_id=that supplied * * @ingroup tripal_cv_api */ function tripal_cv_get_cvterm_options($cv_id = 0) { $previous_db = tripal_db_set_active('chado'); if ($cv_id > 0) { $result = db_query( "SELECT cvterm_id, name FROM cvterm WHERE cv_id=%d", $cv_id ); } else { $result = db_query( "SELECT cvterm_id, name FROM cvterm" ); } tripal_db_set_active($previous_db); $options = array(); while ( $r = db_fetch_object($result) ) { $options[$r->cvterm_id] = $r->name; } return $options; } /** * Implements hook_chado_cvterm_schema() * Purpose: To add descriptions and foreign keys to default table description * Note: This array will be merged with the array from all other implementations * * @return * Array describing the cvterm table * * @ingroup tripal_schema_api */ function tripal_cv_chado_cvterm_schema() { $description = array(); $description['foreign keys']['cv'] = array( 'table' => 'cv', 'columns' => array( 'cv_id' => 'cv_id', ), ); $description['foreign keys']['dbxref'] = array( 'table' => 'dbxref', 'columns' => array( 'dbxref_id' => 'dbxref_id', ), ); return $description; }