tripal_featuremap.DEPRECATED.inc
- 2.x tripal_featuremap/api/tripal_featuremap.DEPRECATED.inc
- 3.x legacy/tripal_featuremap/api/tripal_featuremap.DEPRECATED.inc
Wrapper functions to provide backwards compatibility for the tripal featuremap api
File
tripal_featuremap/api/tripal_featuremap.DEPRECATED.incView source
- <?php
- /**
- * @file
- * Wrapper functions to provide backwards compatibility for the tripal featuremap api
- */
-
- /**
- * @deprecated Restructured API to make naming more readable and consistent.
- * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_get_property().
- *
- * @see chado_get_property().
- */
- function tripal_featuremap_get_property($featuremap_id, $property) {
-
- tripal_report_error(
- 'tripal_deprecated',
- TRIPAL_NOTICE,
- "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
- array(
- '%old_function'=>'tripal_featuremap_get_property',
- '%new_function' => 'chado_get_property'
- )
- );
- $record = array(
- 'table' => 'featuremap',
- 'id' => $featuremap_id,
- );
- $property = array(
- 'type_name' => $property,
- 'cv_name' => 'featuremap_property',
- );
- return chado_get_property($record, $property);
- }
-
- /**
- * @deprecated Restructured API to make naming more readable and consistent.
- * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_insert_property().
- *
- * @see chado_insert_property().
- */
- function tripal_featuremap_insert_property($featuremap_id, $property, $value, $update_if_present = 0) {
-
- tripal_report_error(
- 'tripal_deprecated',
- TRIPAL_NOTICE,
- "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
- array(
- '%old_function'=>'tripal_featuremap_insert_property',
- '%new_function' => 'chado_insert_property'
- )
- );
- $record = array(
- 'table' => 'featuremap',
- 'id' => $featuremap_id,
- );
- $property = array(
- 'type_name' => $property,
- 'cv_name' => 'featuremap_property',
- 'value' => $value,
- );
- $options = array(
- 'update_if_present' => $update_if_present,
- );
- return chado_insert_property($record, $property, $options);
- }
-
- /**
- * @deprecated Restructured API to make naming more readable and consistent.
- * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_update_property().
- *
- * @see chado_update_property().
- */
- function tripal_featuremap_update_property($featuremap_id, $property, $value, $insert_if_missing = 0) {
-
- tripal_report_error(
- 'tripal_deprecated',
- TRIPAL_NOTICE,
- "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
- array(
- '%old_function'=>'tripal_featuremap_update_property',
- '%new_function' => 'chado_update_property'
- )
- );
- $record = array(
- 'table' => 'featuremap',
- 'id' => $featuremap_id,
- );
- $property = array(
- 'type_name' => $property,
- 'cv_name' => 'featuremap_property',
- 'value' => $value,
- );
- $options = array(
- 'insert_if_missing' => $insert_if_missing,
- );
- return chado_update_property($record, $property, $options);
- }
-
- /**
- * @deprecated Restructured API to make naming more readable and consistent.
- * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_delete_property().
- *
- * @see chado_delete_property().
- */
- function tripal_featuremap_delete_property($featuremap_id, $property) {
-
- tripal_report_error(
- 'tripal_deprecated',
- TRIPAL_NOTICE,
- "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
- array(
- '%old_function'=>'tripal_featuremap_delete_property',
- '%new_function' => 'chado_delete_property'
- )
- );
-
- $record = array(
- 'table' => 'featuremap',
- 'id' => $featuremap_id,
- );
- $property = array(
- 'type_name' => $property,
- 'cv_name' => 'featuremap_property',
- );
-
- return chado_delete_property($record, $property);
- }
-
- /**
- * @deprecated Restructured API to make naming more readable and consistent.
- * Function was deprecated in Tripal 2.0 and will be removed 2 releases from now.
- * This function has been replaced by chado_associate_dbxref().
- *
- * @see chado_associate_dbxref().
- */
- function tripal_featuremap_add_featuremap_dbxref($featuremap_id, $featuremap_dbxref) {
-
- tripal_report_error(
- 'tripal_deprecated',
- TRIPAL_NOTICE,
- "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.",
- array(
- '%old_function'=>'tripal_featuremap_add_featuremap_dbxref',
- '%new_function' => 'chado_associate_dbxref'
- )
- );
-
- // break apart the dbxref
- $dbname = '';
- $accession = '';
- if(preg_match('/^(.*?):(.*?)$/', $featuremap_dbxref, $matches)) {
- $dbname = $matches[1];
- $accession = $matches[2];
- }
- else {
- return FALSE;
- }
-
- // check to see if the featuremap_dbxref record already exist
- $values = array(
- 'dbxref_id' => array(
- 'accession' => $accession,
- 'db_id' => array(
- 'name' => $dbname,
- ),
- ),
- 'featuremap_id' => $featuremap_id,
- );
- $options = array('statement_name' => 'sel_featuremapdbxref_dbpu');
- $results = chado_select_record('featuremap_dbxref', array('*'), $values, $options);
-
- // if the featuremap_dbxref record exist then we don't need to re-add it.
- if(count($results) > 0) {
- return $results[0];
- }
-
- // make sure our database already exists
- $db = tripal_db_add_db($dbname);
-
- // get the database cross-reference
- $dbxvalues = array(
- 'accession' => $accession,
- 'db_id' => $db->db_id,
- );
- $dbxoptions = array('statement_name' => 'sel_dbxref_acdb');
- $results = chado_select_record('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions);
- // if the accession doesn't exist then add it
- if(count($results) == 0){
- $dbxref = tripal_db_add_dbxref($db->db_id, $accession);
- }
- else {
- $dbxref = $results[0];
- }
-
- // now add the record
- $options = array('statement_name' => 'ins_featuremapdbxref_dbpu');
- $results = chado_insert_record('featuremap_dbxref', $values, $options);
- if (!$results) {
- tripal_report_error('t_featuremap', TRIPAL_ERROR, "Cannot add map dbxref: %db:%accession.",
- array('%db' => $dbname, '%accession' => $accession));
- return FALSE;
- }
- return $results;
- }