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- <?php
- 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
- );
- }
-
- }
- 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 $r;
- }
- function tripal_cv_get_cv_by_id ($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;
- }
- 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 $options;
- }
- function tripal_cv_get_cvterm ($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) {
-
- $cvterm = tripal_cv_add_cv_to_object(array('cv_id'=>$results[0]->cv_id),$results[0],array());
- unset($cvterm->cv_id);
-
-
- $cvterm = tripal_db_add_dbxref_to_object(array('dbxref_id'=>$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
- );
- }
-
- }
- 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 $r;
-
- }
- function tripal_cv_get_cvterm_options($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;
- }
- 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 $description;
- }
- function tripal_cv_add_cv($name,$comment){
-
- $vocab = $name;
- $remark = $comment;
- $cv_sql = "SELECT * FROM {cv} WHERE name = '%s'";
- $cv = db_fetch_object(db_query($cv_sql,$vocab));
-
- if(!$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 $cv;
- }
- function tripal_cv_add_cvterm($term,$defaultcv,$is_relationship = 0,$update = 1){
-
- $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){
- $is_obsolete = 1;
- }
- if(!$cvname){
- $cvname = $defaultcv->name;
- }
-
- $cv = tripal_cv_add_cv($cvname,'');
- if(!$cv){
- watchdog('tripal_cv', "Cannot find namespace '$cvname' when adding/updating $id",NULL,WATCHDOG_WARNING);
- return 0;
- }
-
-
- $cvtermsql = "SELECT CVT.name, CVT.cvterm_id, DB.name as dbname, DB.db_id
- FROM {cvterm} CVT
- INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
- INNER JOIN {db} DB on DBX.db_id = DB.db_id
- INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
- WHERE CVT.name = '%s' and DB.name = '%s'";
-
- if(preg_match('/^.+?:.*$/',$id)){
- $accession = preg_replace('/^.+?:(.*)$/','\1',$id);
- $dbname = preg_replace('/^(.+?):.*$/','\1',$id);
- }
- if($is_relationship and !$dbname){
- $accession = $id;
-
-
-
- $cvterm = db_fetch_object(db_query($cvtermsql,$name,'OBO_REL'));
- if($cvterm){
- return $cvterm;
- } else {
-
-
- $dbname = '_global';
- $cvterm = db_fetch_object(db_query($cvtermsql,$name,$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;
- }
-
- $db = tripal_db_add_db($dbname);
- if(!$db){
- watchdog('tripal_cv', "Cannot find database '$dbname' in Chado.",NULL,WATCHDOG_WARNING);
- return 0;
- }
-
- $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname));
- if(!$cvterm){
-
- $dbxref = tripal_db_add_dbxref($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;
- }
-
- $sql = "SELECT * FROM {cvterm} WHERE dbxref_id = %d";
- $check = db_fetch_object(db_query($sql,$dbxref->dbxref_id));
- if(!$check){
-
- $sql = "
- INSERT INTO {cvterm} (cv_id, name, definition, dbxref_id,
- is_obsolete, is_relationshiptype)
- VALUES (%d,'%s','%s',%d,%d,%d)
- ";
- if(!db_query($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: $dbname)",NULL,WATCHDOG_WARNING);
- return 0;
- }
- }
- }
- elseif($check and strcmp($check->name,$name)==0){
-
- }
- elseif($check and strcmp($check->name,$name)!=0){
- watchdog('tripal_cv', "The dbxref already exists in the cvterm table: $dbxref->dbxref_id ($$accession) for term $name",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) {
- $sql = "
- UPDATE {cvterm} SET name='%s', definition='%s',
- is_obsolete = %d, is_relationshiptype = %d
- WHERE cvterm_id = %d
- ";
- if(!db_query($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 $cvterm;
- }
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