'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) /** * Retrieve a cv given the cv name * * @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; } /** * Retrieve the cv object for the specified CV id * * NOTE: This function is deprecated. * @see tripal_core_chado_generate_vars * * @param $cv_id * The unique identifier for the cv retrieve * * @return * An object describing the cv * * @ingroup tripal_cv_api */ function tripal_cv_get_cv_by_id ($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; } /** * 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; } /** * 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 * @param $cv_name * the name of the CV * * @return * cvterm object * * @ingroup tripal_cv_api */ function tripal_cv_get_cvterm_by_name ($name, $cv_id=0,$cv_name='tripal') { if ($cv_id) { $values = array( 'name' => $name, 'cv_id' => $cv_id, ); $r = tripal_core_chado_select('cvterm',array('*'),$values); } elseif($cv_name){ $values = array( 'name' => $name, 'cv_id' => array( 'name' => $cv_name, ), ); $r = tripal_core_chado_select('cvterm',array('*'),$values); } else { $values = array( 'name' => $name, ); $r = tripal_core_chado_select('cvterm',array('*'),$values); } if(!$r){ return FALSE; } if(count($r) > 0){ return FALSE; } return $r[0]; } /** * 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; } /** * Adds a controlled vocabular to the CV table of Chado. * * @param $name * The name of the controlled vocabulary. These are typically all lower case * with no special characters other than an undrescore (for spaces). * @param $comment * A description or definition of the vocabulary. * * @return * An object populated with fields from the newly added database. * * @ingroup tripal_cv_api */ function tripal_cv_add_cv($name,$comment){ // see if the CV (default-namespace) exists already in the database $vocab = $name; $remark = $comment; $cv_sql = "SELECT * FROM {cv} WHERE name = '%s'"; $cv = db_fetch_object(db_query($cv_sql,$vocab)); // if the CV exists then update it, otherwise insert if(!$cv){ $sql = "INSERT INTO {cv} (name,definition) VALUES ('%s','%s')"; if(!db_query($sql,$vocab,$remark)){ watchdog('tripal_cv', "Failed to create the CV record",NULL,WATCHDOG_WARNING); return 0; } $cv = db_fetch_object(db_query($cv_sql,$vocab)); } else { $sql = "UPDATE {cv} SET definition = '%s' WHERE name ='%s'"; if(!db_query($sql,$remark,$vocab)){ watchdog('tripal_cv', "Failed to update the CV record",NULL,WATCHDOG_WARNING); return 0; } $cv = db_fetch_object(db_query($cv_sql,$vocab)); } return $cv; } /** * Add's a CV term to the cvterm table. If the parent CV does not exist then * that too is added to the CV table. If the cvterm is a relationship term * then the $is_relationship argument should be set. The function will try * to first find the relationship in the relationship ontology for updating and * if it can't be found will add the relationship to the __global CV. All terms * must also have a corresponding database. This is specified in the term's * ID just before the colon (e.g. GO:003824). If the database does not exist * in the DB table then it will be added automatically. The accession (the * value just after the colon in the term's ID) will be added to the dbxref * table. If the CVterm already exists and $update is set (default) then the * cvterm is updated. If the CVTerm already exists and $update is not set, then * no changes are made and the CVTerm object is returned. * * @param $term * An associative array with the following keys: 'id', 'name' and 'namespace', * 'is_obsolete', and 'def'. Where 'id' is the term accession, 'name' is the * term name, 'namespace' is the CV name for the term, 'def' is the term * definition and 'is_obsolete' is present and set to 1 if the term is defunct. * The 'id' must be of the form :, where is the name of * the database to which the cvterm belongs and the is the * term's accession number in the database. * @param $defaultcv * Optional. The CV name to which the term * belongs. If this arugment is null or not provided then the function tries * to find a record in the CV table with the same name provided in the * $term[namespace]. If this field is provided then it overrides what the * value in $term[namespace] * @param $is_relationship * If this term is a relationship term then this value should be 1. * @param $update * By default this is set to 1. If the term exists it is automatically updated. * @param $dbname * In some cases the database name will not be part of the $term['id'] and it * needs to be explicitly set. Use this argument only if the database name * cannot be specififed in the term ID (e.g. :). * * @return * A CVTerm object * * @ingroup tripal_cv_api */ function tripal_cv_add_cvterm($term,$defaultcv='',$is_relationship = 0,$update = 1,$dbname=NULL){ // get the term properties $id = $term['id']; $name = $term['name']; $cvname = $term['namespace']; $definition = preg_replace('/^\"(.*)\"/','\1',$term['def']); $is_obsolete = 0; if(isset($term['is_obsolete']) and strcmp($term['is_obsolete'],'true')==0){ $is_obsolete = 1; } if(!$name and !$id){ watchdog('tripal_cv', "Cannot find cvterm without 'id' or 'name'",NULL,WATCHDOG_WARNING); return 0; } if(!$id){ $id = $name; } if(!$name){ $name = $id; } if(!$cvname){ $cvname = $defaultcv; } // make sure the CV name exists $cv = tripal_cv_add_cv($cvname,''); if(!$cv){ watchdog('tripal_cv', "Cannot find namespace '$cvname' when adding/updating $id",NULL,WATCHDOG_WARNING); return 0; } // this SQL statement will be used a lot to find a cvterm so just set it // here for easy reference below. Because CV terms can change their names // but accessions don't change, the following SQL finds cvterms based on // their accession rather than the name $cvtermsql = "SELECT CVT.name, CVT.cvterm_id, DB.name as dbname, DB.db_id FROM {cvterm} CVT INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id INNER JOIN {db} DB on DBX.db_id = DB.db_id INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id WHERE DBX.accession = '%s' and DB.name = '%s'"; // get the accession and the database from the cvterm if($dbname){ $accession = $id; } elseif(preg_match('/^.+?:.*$/',$id)){ $accession = preg_replace('/^.+?:(.*)$/','\1',$id); $dbname = preg_replace('/^(.+?):.*$/','\1',$id); } if($is_relationship and !$dbname){ $accession = $id; // because this is a relationship cvterm first check to see if it // exists in the relationship ontology. If it does then return the cvterm. // If not then set the dbname to _global and we'll add it or find it there $cvterm = db_fetch_object(db_query($cvtermsql,$accession,'OBO_REL')); if($cvterm){ return $cvterm; } else { // next check if this term is in the _global ontology. If it is then // return it no matter what the original CV $dbname = '_global'; $cvterm = db_fetch_object(db_query($cvtermsql,$accesion,$dbname)); if($cvterm){ return $cvterm; } } } if(!$is_relationship and !$dbname){ watchdog('tripal_cv', "A database identifier is missing from the term: $id",NULL,WATCHDOG_WARNING); return 0; } // add the database. The function will just return the DB object if the // database already exists. $db = tripal_db_add_db($dbname); if(!$db){ watchdog('tripal_cv', "Cannot find database '$dbname' in Chado.",NULL,WATCHDOG_WARNING); return 0; } // if the cvterm doesn't exist then add it otherwise just update it $cvterm = db_fetch_object(db_query($cvtermsql,$accession,$dbname)); if(!$cvterm){ // check to see if the dbxref exists if not, add it $dbxref = tripal_db_add_dbxref($db->db_id,$accession); if(!$dbxref){ watchdog('tripal_cv', "Failed to find or insert the dbxref record for cvterm, $name (id: $accession), for database $dbname",NULL,WATCHDOG_WARNING); return 0; } // check to see if the dbxref already has an entry in the cvterm table $sql = "SELECT * FROM {cvterm} WHERE dbxref_id = %d"; $check = db_fetch_object(db_query($sql,$dbxref->dbxref_id)); if(!$check){ // now add the cvterm $sql = " INSERT INTO {cvterm} (cv_id, name, definition, dbxref_id, is_obsolete, is_relationshiptype) VALUES (%d,'%s','%s',%d,%d,%d) "; if(!db_query($sql,$cv->cv_id,$name,$definition, $dbxref->dbxref_id,$is_obsolete,$is_relationship)){ if(!$is_relationship){ watchdog('tripal_cv', "Failed to insert the term: $name ($dbname)",NULL,WATCHDOG_WARNING); return 0; } else { watchdog('tripal_cv', "Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)",NULL,WATCHDOG_WARNING); return 0; } } } // if the dbxref already exists check to make sure it exists for the correct databaes name // if it does then we're good and we don't need to do anything elseif($check and strcmp($check->name,$name)==0){ // this entry already exists. We're good, so do nothing } // if the dbxref exists but does not map to the same database name elseif($check and strcmp($check->name,$name)!=0){ watchdog('tripal_cv', "The dbxref already exists in the cvterm table. DBXREF ID: $dbxref->dbxref_id, ACCESSION: $accession. DB: '".$dbxref->db_name ."'. term '$name'. The requested db was '$dbname'",NULL,WATCHDOG_WARNING); return 0; } $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname)); if(!$is_relationship){ print "Added CV term: $name ($dbname)\n"; } else { print "Added relationship CV term: $name ($dbname)\n"; } } elseif($update) { // update the cvterm $sql = " UPDATE {cvterm} SET name='%s', definition='%s', is_obsolete = %d, is_relationshiptype = %d WHERE cvterm_id = %d "; if(!db_query($sql,$term['name'],$definition, $is_obsolete,$is_relationship,$cvterm->cvterm_id)){ watchdog('tripal_cv', "Failed to update the term: $name",NULL,WATCHDOG_WARNING); return 0; } $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname)); if(!$is_relationship){ print "Updated CV term: $name ($dbname)\n"; } else { print "Updated relationship CV term: $name ($dbname)\n"; } } // return the cvterm return $cvterm; }