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@@ -108,180 +108,120 @@ require_once "tripal_core.schema.api.inc";
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*
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* @ingroup tripal_chado_api
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*/
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-function tripal_core_chado_insert($table, $values, $options = array()){
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- $chado_db = tripal_db_persistent_chado();
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-
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- // Determine plan of action
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- if ($options['statement_name']) {
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- $prepared = TRUE;
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- if ($options['prepare']) {
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- $build_sql = TRUE;
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- } else {
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- $build_sql = FALSE;
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- }
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- } else {
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- $build_sql = TRUE;
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- }
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-
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- // get the table description
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- $table_desc = module_invoke_all('chado_'.$table.'_schema');
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- if (empty($table_desc)) {
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- watchdog('tripal_core', 'tripal_core_chado_insert: There is no table description for !table_name', array('!table_name' => $table), WATCHDOG_WARNING);
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- }
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-
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- // iterate through the values array and create a new 'insert_values' array
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- // that has all the values needed for insert with all foreign relationsihps
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- // resolved.
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- $insert_values = array();
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- foreach($values as $field => $value){
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- if(is_array($value)){
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- // select the value from the foreign key relationship for this value
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- $results = tripal_core_chado_get_foreign_key($table_desc,$field,$value);
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- if (sizeof($results) > 1) {
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- watchdog('tripal_core', 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
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- } elseif (sizeof($results) < 1) {
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- //watchdog('tripal_core', 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
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- } else {
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- $insert_values[$field] = $results[0];
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- }
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- }
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- else {
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- $insert_values[$field] = $value;
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- }
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- }
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-
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- // check for violation of any unique constraints
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- $ukeys = $table_desc['unique keys'];
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- $ukselect_cols = array();
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- $ukselect_vals = array();
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- if ($ukeys) {
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- foreach($ukeys as $name => $fields){
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- foreach($fields as $index => $field){
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- // build the arrays for performing a select that will check the contraint
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- array_push($ukselect_cols,$field);
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- $ukselect_vals[$field] = $insert_values[$field];
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+function tripal_core_chado_insert($table,$values){
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+ $insert_values = array();
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+
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+ // get the table description
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+ $table_desc = module_invoke_all('chado_'.$table.'_schema');
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+ if (empty($table_desc)) {
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+ watchdog('tripal_core', 'tripal_core_chado_insert: There is no table description for !table_name', array('!table_name' => $table), WATCHDOG_WARNING);
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+ }
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+
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+ // iterate through the values array and create a new 'insert_values' array
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+ // that has all the values needed for insert with all foreign relationsihps
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+ // resolved.
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+ foreach($values as $field => $value){
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+ if(is_array($value)){
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+ // select the value from the foreign key relationship for this value
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+ $results = tripal_core_chado_get_foreign_key($table_desc,$field,$value);
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+ if (sizeof($results) > 1) {
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+ watchdog('tripal_core', 'tripal_core_chado_insert: Too many records match the criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
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+ } elseif (sizeof($results) < 1) {
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+ //watchdog('tripal_core', 'tripal_core_chado_insert: no record matches criteria supplied for !foreign_key foreign key constraint (!criteria)', array('!foreign_key' => $field, '!criteria' => print_r($value,TRUE)), WATCHDOG_ERROR);
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+ } else {
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+ $insert_values[$field] = $results[0];
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+ }
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+ }
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+ else {
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+ $insert_values[$field] = $value;
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}
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- // now check the constraint
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- if(tripal_core_chado_select($table,$ukselect_cols,$ukselect_vals)){
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- watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate record into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
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+ }
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+
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+ // check for violation of any unique constraints
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+ $ukeys = $table_desc['unique keys'];
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+ $ukselect_cols = array();
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+ $ukselect_vals = array();
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+ if ($ukeys) {
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+ foreach($ukeys as $name => $fields){
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+ foreach($fields as $index => $field){
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+ // build the arrays for performing a select that will check the contraint
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+ array_push($ukselect_cols,$field);
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+ $ukselect_vals[$field] = $insert_values[$field];
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+ }
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+ // now check the constraint
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+ if(tripal_core_chado_select($table,$ukselect_cols,$ukselect_vals)){
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+ watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate record into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
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+ return false;
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+ }
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+ }
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+ }
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+
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+ // if trying to insert a field that is the primary key, make sure it also is unique
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+ $pkey = $table_desc['primary key'][0];
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+ if($insert_values[$pkey]){
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+ if(tripal_core_chado_select($table,array($pkey),array($pkey => $insert_values[$pkey]))){
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+ watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
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return false;
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}
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}
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- }
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-
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- // if trying to insert a field that is the primary key, make sure it also is unique
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- $pkey = $table_desc['primary key'][0];
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- if($insert_values[$pkey]){
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- if(tripal_core_chado_select($table,array($pkey),array($pkey => $insert_values[$pkey]))){
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- watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
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- return false;
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- }
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- }
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-
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- // make sure required fields have a value
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- $fields = $table_desc['fields'];
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- if (!is_array($fields)) {
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- $fields = array();
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- watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
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- }
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- foreach($fields as $field => $def){
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- // a field is considered missing if it cannot be null and there is no default
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- // value for it or it is of type 'serial'
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- if($def['not null'] == 1 and !array_key_exists($field,$insert_values) and !isset($def['default']) and strcmp($def['type'],serial)!=0){
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- watchdog('tripal_core',"tripal_core_chado_insert: Field $table.$field cannot be null: " . print_r($values,1),array(),'WATCHDOG_ERROR');
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- return false;
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- }
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- }
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-
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- // Now build the insert SQL statement
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- $ifields = array();
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- $ivalues = array();
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- $itypes = array();
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- $iplaceholders = array();
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- $i = 1;
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- foreach ($insert_values as $field => $value){
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- array_push($ifields,$field);
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- array_push($ivalues,$value);
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- array_push($iplaceholders,'$'.$i);
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- $i++;
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- if(strcmp($value,'__NULL__')==0){
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- array_push($itypes,"NULL");
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- }
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- elseif(strcmp($fields[$field]['type'],'serial')==0 or
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- strcmp($fields[$field]['type'],'int')==0){
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- array_push($itypes,"%d");
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- }
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- else {
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- array_push($itypes,"'%s'");
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- }
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- }
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- if ($build_sql) {
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- // prepare the statement
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- if ($prepared) {
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- $sql = "INSERT INTO {$table} (" . implode(", ",$ifields) . ") VALUES (". implode(", ",$iplaceholders) .")";
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-
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- $previous_db = tripal_db_set_active('chado');
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- $status = pg_prepare($chado_db, $options['statement_name'], $sql);
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- tripal_db_set_active($previous_db);
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-
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- if (!$status) {
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- watchdog('tripal_core',"tripal_core_chado_insert: not able to prepare '%name' statement for: %sql", array('%name' => $options['statement_name'], '%sql' => $sql), 'WATCHDOG ERROR');
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- return FALSE;
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+ // make sure required fields have a value
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+ $fields = $table_desc['fields'];
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+ if (!is_array($fields)) {
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+ $fields = array();
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+ watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
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+ }
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+ foreach($fields as $field => $def){
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+ // a field is considered missing if it cannot be null and there is no default
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+ // value for it or it is of type 'serial'
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+ if($def['not null'] == 1 and !array_key_exists($field,$insert_values) and !isset($def['default']) and strcmp($def['type'],serial)!=0){
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+ watchdog('tripal_core',"tripal_core_chado_insert: Field $table.$field cannot be null: " . print_r($values,1),array(),'WATCHDOG_ERROR');
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+ return false;
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}
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- } else {
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- $sql = "INSERT INTO {$table} (" . implode(", ",$ifields) . ") VALUES (". implode(", ",$itypes) .")";
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- }
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-
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- }
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-
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- // finally perform the insert.
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- if ($prepared) {
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-
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- $previous_db = tripal_db_set_active('chado');
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- $result = pg_execute($chado_db, $options['statement_name'], $ivalues);
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- tripal_db_set_active($previous_db);
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- if ($result) {
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- // add primary keys to values before return
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- $primary_key = array();
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- if (!is_array($table_desc['primary key'])) {
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- $table_desc['primary key'] = array();
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- watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
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- }
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- foreach ($table_desc['primary key'] as $field) {
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- $value = db_last_insert_id($table, $field);
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- $values[$field] = $value;
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- }
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- return $values;
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- } else {
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- watchdog('tripal_core',"tripal_core_chado_insert: not able to execute prepared statement '%name' with values: %values", array('%name' => $options['statement_name'], '%values' => print_r($values,1)), 'WATCHDOG ERROR');
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- return FALSE;
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+ }
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+
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+ // Now build the insert SQL statement
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+ $ifields = array();
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+ $ivalues = array();
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+ $itypes = array();
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+ foreach ($insert_values as $field => $value){
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+ array_push($ifields,$field);
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+ array_push($ivalues,$value);
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+ if(strcmp($value,'__NULL__')==0){
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+ array_push($itypes,"NULL");
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+ }
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+ elseif(strcmp($fields[$field]['type'],'serial')==0 or
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+ strcmp($fields[$field]['type'],'int')==0){
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+ array_push($itypes,"%d");
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+ }
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+ else {
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+ array_push($itypes,"'%s'");
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}
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+ }
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+ $sql = "INSERT INTO {$table} (" . implode(", ",$ifields) . ") VALUES (". implode(", ",$itypes) .")";
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- } else {
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- $previous_db = tripal_db_set_active('chado'); // use chado database
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- $result = db_query($sql,$ivalues);
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- tripal_db_set_active($previous_db); // now use drupal database
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- if($result){
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+ // finally perform the insert.
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+ $previous_db = tripal_db_set_active('chado'); // use chado database
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+ $result = db_query($sql,$ivalues);
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+ tripal_db_set_active($previous_db); // now use drupal database
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+ if($result){
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// add primary keys to values before return
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$primary_key = array();
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if (!is_array($table_desc['primary key'])) {
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- $table_desc['primary key'] = array();
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- watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
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+ $table_desc['primary key'] = array();
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+ watchdog('tripal_core',"tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
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}
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foreach ($table_desc['primary key'] as $field) {
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$value = db_last_insert_id($table, $field);
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$values[$field] = $value;
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}
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return $values;
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- }
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- else {
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+ }
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+ else {
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watchdog('tripal_core',"tripal_core_chado_insert: Cannot insert record into $table table: " . print_r($values,1),array(),'WATCHDOG_ERROR');
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return false;
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- }
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- }
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-
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- return false;
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+ }
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+ return false;
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}
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/**
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@@ -655,7 +595,7 @@ function tripal_core_chado_select($table,$columns,$values,$options = null){
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'case_insensitive_columns' => $options['case_insensitive_columns']
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);
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$results = tripal_core_chado_get_foreign_key($table_desc,$field,$value, $foreign_options);
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- if (sizeof($results) < 1) {
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+ if (count($results) ==0) {
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// foreign key records are required
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// thus if none matched then return false and alert the admin through watchdog
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//watchdog('tripal_core',
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@@ -819,10 +759,12 @@ function tripal_core_chado_get_foreign_key($table_desc,$field,$values, $options
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$select_cols = array($right);
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$result = tripal_core_chado_select($table,$select_cols,$values, $options);
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$fields = array();
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- foreach ($result as $obj) {
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- $fields[] = $obj->$right;
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+ if(count($result) > 0){
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+ foreach ($result as $obj) {
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+ $fields[] = $obj->$right;
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+ }
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+ return $fields;
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}
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- return $fields;
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}
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}
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}
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@@ -1419,19 +1361,22 @@ function chado_get_node_id ($table, $id) {
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* The base table for which the property should be retrieved. Thus to retrieve a property
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* for a feature the basetable=feature and property is retrieved from featureprop
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* @param $record_id
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- * The primary key of the basetable to retrieve properties for. This should be in integer.
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+ * The foriegn key field of the base table. This should be in integer.
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* @param $property
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* The cvterm name describing the type of properties to be retrieved
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* @param $cv_name
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* The name of the cv that the above cvterm is part of
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*
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* @return
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- * A chado variable with the specified properties expanded
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+ * An array in the same format as that generated by the function
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+ * tripal_core_generate_chado_var(). If only one record is returned it
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+ * is a single object. If more than one record is returned then it is an array
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+ * of objects
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*
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* @ingroup tripal_chado_api
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*/
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function tripal_core_get_property($basetable, $record_id, $property, $cv_name){
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-
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+
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// get the foreign key for this property table
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$table_desc = module_invoke_all('chado_'.$basetable.'prop_schema');
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$fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
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@@ -1447,6 +1392,7 @@ function tripal_core_get_property($basetable, $record_id, $property, $cv_name){
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'is_obsolete' => 0
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),
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);
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+
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$results = tripal_core_generate_chado_var($basetable.'prop',$values);
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$results = tripal_core_expand_chado_vars($results,'field',$basetable.'prop.value');
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return $results;
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@@ -1461,7 +1407,7 @@ function tripal_core_get_property($basetable, $record_id, $property, $cv_name){
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* The base table for which the property should be inserted. Thus to insert a property
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* for a feature the basetable=feature and property is inserted into featureprop
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* @param $record_id
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- * The primary key of the basetable to insert a property for. This should be in integer.
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+ * The foriegn key field of the base table. This should be in integer.
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* @param $property
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* The cvterm name describing the type of properties to be inserted
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* @param $cv_name
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@@ -1484,17 +1430,25 @@ function tripal_core_insert_property($basetable, $record_id, $property,
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// first see if the property already exists, if the user want's to update
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// then we can do that, but otherwise we want to increment the rank and
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// insert
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- $prop = tripal_core_get_property($basetable,$record_id,$property,$cv_name);
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+ $props = tripal_core_get_property($basetable,$record_id,$property,$cv_name);
|
|
|
+ if(!is_array($props)) {
|
|
|
+ $props = array($props);
|
|
|
+ }
|
|
|
$rank = 0;
|
|
|
- if(count($prop)>0){
|
|
|
+ if(count($props)>0){
|
|
|
if($update_if_present){
|
|
|
- return tripal_core_update_property($basetable,$record_id,$property,$cv_name,$value) ;
|
|
|
+ return tripal_core_update_property($basetable, $record_id, $property, $cv_name, $value) ;
|
|
|
} else {
|
|
|
- // iterate through the properties returned and get the largest rank
|
|
|
- foreach($prop as $p){
|
|
|
+ // iterate through the properties returned and check to see if the
|
|
|
+ // property with this value already exists if not, get the largest rank
|
|
|
+ // and insert the same property but with this new value
|
|
|
+ foreach($props as $p){
|
|
|
if($p->rank > $rank){
|
|
|
$rank = $p->rank;
|
|
|
}
|
|
|
+ if(strcmp($p->value,$value)==0){
|
|
|
+ return TRUE;
|
|
|
+ }
|
|
|
}
|
|
|
// now add 1 to the rank
|
|
|
$rank++;
|
|
|
@@ -1791,47 +1745,6 @@ function tripal_db_set_active($dbname){
|
|
|
}
|
|
|
else return db_set_active($dbname);
|
|
|
}
|
|
|
-
|
|
|
-/**
|
|
|
- * Instantiate or Return a persistent chado connection
|
|
|
- *
|
|
|
- * NOTE: cannot use $active_db since a new connection is created each time
|
|
|
- * db_set_active() is called
|
|
|
- *
|
|
|
- * @return
|
|
|
- * A postgresql connection object which can be used by pg_prepare, pg_execute, etc.
|
|
|
- */
|
|
|
-function tripal_db_persistent_chado () {
|
|
|
- global $db_url;
|
|
|
-
|
|
|
- // get connection if it already exists
|
|
|
- $connection = variable_get('tripal_perisistent_chado',NULL);
|
|
|
-
|
|
|
- if ($connection) {
|
|
|
- return $connection;
|
|
|
-
|
|
|
- // Otherwise we need to set it
|
|
|
- } else {
|
|
|
- if (is_array($db_url) && isset($db_url['chado'])) {
|
|
|
- $connection = db_connect($db_url['chado']);
|
|
|
- variable_set('tripal_perisistent_chado', $connection);
|
|
|
- } else {
|
|
|
- $connection = db_connect($db_url);
|
|
|
- variable_set('tripal_perisistent_chado', $connection);
|
|
|
- }
|
|
|
-
|
|
|
- return $connection;
|
|
|
- }
|
|
|
- return FALSE;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Release a persistent chado connection
|
|
|
- */
|
|
|
-function tripal_db_release_persistent_chado () {
|
|
|
- variable_del('tripal_perisistent_chado');
|
|
|
-}
|
|
|
-
|
|
|
/**
|
|
|
* Purpose: Get max rank for a given set of criteria
|
|
|
* This function was developed with the many property tables in chado in mind
|
|
|
@@ -1884,3 +1797,101 @@ function tripal_get_max_chado_rank ($tablename, $where_options) {
|
|
|
return -1;
|
|
|
}
|
|
|
}
|
|
|
+/**
|
|
|
+ * Add a new table to the Chado schema. This function is simply a wrapper for
|
|
|
+ * the db_create_table() function of Drupal, but ensures the table is created
|
|
|
+ * inside the Chado schema rather than the Drupal schema. If the table already
|
|
|
+ * exists then it will be dropped and recreated using the schema provided.
|
|
|
+ * Howver, it will only drop a table if it exsits in the tripal_custom_tables
|
|
|
+ * table. This way the function cannot be used to accidentally alter existing
|
|
|
+ * non custom tables.
|
|
|
+ *
|
|
|
+ * @param $ret
|
|
|
+ * Array to which query results will be added.
|
|
|
+ * @param $table
|
|
|
+ * The name of the table to create.
|
|
|
+ * @param $schema
|
|
|
+ * A Drupal-style Schema API definition of the table
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A database query result resource for the new table, or FALSE if table was not constructed.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_core_api
|
|
|
+ */
|
|
|
+function tripal_create_chado_table (&$ret,$table,$schema) {
|
|
|
+ $ret = array();
|
|
|
+
|
|
|
+ // If the table exits in Chado but not in the tripal_custom_tables field
|
|
|
+ // then call an error. if the table exits in the tripal_custom_tables but
|
|
|
+ // not in Chado then create the table and replace the entry.
|
|
|
+ $sql = "SELECT * FROM {tripal_custom_tables} WHERE table_name = '%s'";
|
|
|
+ $centry = db_fetch_object(db_query($sql,$table));
|
|
|
+ $previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
+ $exists = db_table_exists($table);
|
|
|
+ tripal_db_set_active($previous_db); // now use drupal database
|
|
|
+ if(!$exists){
|
|
|
+ $previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
+ db_create_table($ret,$table,$schema);
|
|
|
+ tripal_db_set_active($previous_db); // now use drupal database
|
|
|
+ if(count($ret)==0){
|
|
|
+ watchdog('tripal_core', "Error adding custom table '!table_name'.",
|
|
|
+ array('!table_name' => $table), WATCHDOG_ERROR);
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if($exists and !$centry){
|
|
|
+ watchdog('tripal_core', "Could not add custom table '!table_name'. It ".
|
|
|
+ "already exists but is not known to Tripal as being a custom table.",
|
|
|
+ array('!table_name' => $table), WATCHDOG_WARNING);
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ if($exists and $centry){
|
|
|
+ // drop the table we'll recreate it with the new schema
|
|
|
+ $previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
+ db_drop_table($ret,$table);
|
|
|
+ db_create_table($ret,$table,$schema);
|
|
|
+ tripal_db_set_active($previous_db); // now use drupal database
|
|
|
+ }
|
|
|
+
|
|
|
+ // if the table creation was succesful then add an entry
|
|
|
+ // in the tripal_custom_table
|
|
|
+ $record = new stdClass();
|
|
|
+ $record->table_name = $table;
|
|
|
+ $record->schema = serialize($schema);
|
|
|
+ // if an entry already exists then remove it
|
|
|
+ if($centry){
|
|
|
+ $sql = "DELETE FROM {tripal_custom_tables} WHERE table_name = '%s'";
|
|
|
+ db_query($sql,$table);
|
|
|
+ }
|
|
|
+ $success = drupal_write_record('tripal_custom_tables',$record);
|
|
|
+ if(!$success){
|
|
|
+ watchdog('tripal_core', "Error adding custom table.",
|
|
|
+ array('!table_name' => $table), WATCHDOG_ERROR);
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ return $ret;
|
|
|
+}
|
|
|
+/**
|
|
|
+ * Retrieves the schema in an array for the specified custom table.
|
|
|
+ *
|
|
|
+ * @param $table
|
|
|
+ * The name of the table to create.
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * A Drupal-style Schema API array definition of the table. Returns
|
|
|
+ * FALSE on failure.
|
|
|
+ *
|
|
|
+ * @ingroup tripal_core_api
|
|
|
+ */
|
|
|
+function tripal_get_chado_custom_schema ($table) {
|
|
|
+ $sql = "SELECT schema FROM {tripal_custom_tables} WHERE table_name = '%s'";
|
|
|
+ $custom = db_fetch_object(db_query($sql,$table));
|
|
|
+ if(!$custom){
|
|
|
+ return FALSE;
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ return unserialize($custom->schema);
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+
|
Lacey Sanderson