Skip to content

Commit

Permalink
Merge pull request #1537 from tripal/tv4g0-issue1536-chado_get_organi…
Browse files Browse the repository at this point in the history 
…sm_id_from_scientific_name

Tripal 4 port of tripal 3 chado_get_organism_id_from_scientific_name()
  • Loading branch information
@dsenalik
dsenalik committed Jun 14, 2023
2 parents 27433f6 + 3bbe842 commit 0e78c14
Show file tree
Hide file tree
Showing 5 changed files with 352 additions and 119 deletions.
46 changes: 38 additions & 8 deletions tripal_chado/src/api/tripal_chado.cv.api.php
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,14 +46,19 @@
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cv($identifiers, $options = [], $schema_name = 'chado') {
function chado_get_cv($identifiers, $options = [], $schema_name = NULL) {

// Set Defaults.
// Set default options.
if (!isset($options['include_fk'])) {
// Tells chado_generate_var not to follow any foreign keys.
$options['include_fk'] = [];
}

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Error Checking of parameters.
if (!is_array($identifiers)) {
tripal_report_error(
Expand Down Expand Up @@ -131,7 +136,12 @@ function chado_get_cv($identifiers, $options = [], $schema_name = 'chado') {
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cv_select_options($schema_name = 'chado') {
function chado_get_cv_select_options($schema_name = NULL) {

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

$results = chado_select_record(
'cv',
Expand Down Expand Up @@ -190,14 +200,19 @@ function chado_get_cv_select_options($schema_name = 'chado') {
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cvterm($identifiers, $options = [], $schema_name = 'chado') {
function chado_get_cvterm($identifiers, $options = [], $schema_name = NULL) {

// Set Defaults.
// Set default options.
if (!isset($options['include_fk'])) {
// Tells chado_generate_var to only get the cv.
$options['include_fk'] = ['cv_id' => TRUE];
}

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Error Checking of parameters.
if (!is_array($identifiers)) {
tripal_report_error('tripal_cv_api', TRIPAL_ERROR,
Expand Down Expand Up @@ -331,7 +346,12 @@ function chado_get_cvterm($identifiers, $options = [], $schema_name = 'chado') {
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cvterm_select_options($cv_id, $rel_type = FALSE, $schema_name = 'chado') {
function chado_get_cvterm_select_options($cv_id, $rel_type = FALSE, $schema_name = NULL) {
// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

$columns = ['cvterm_id', 'name'];
$values = ['cv_id' => $cv_id];
if ($rel_type) {
Expand Down Expand Up @@ -369,7 +389,12 @@ function chado_get_cvterm_select_options($cv_id, $rel_type = FALSE, $schema_name
*
* @ingroup tripal_chado_cv_api
*/
function chado_insert_cv($name, $definition, $options = [], $schema_name = 'chado') {
function chado_insert_cv($name, $definition, $options = [], $schema_name = NULL) {

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Insert/update values.
$ins_values = [
Expand Down Expand Up @@ -450,7 +475,12 @@ function chado_insert_cv($name, $definition, $options = [], $schema_name = 'chad
*
* @ingroup tripal_chado_cv_api
*/
function chado_insert_cvterm($term, $options = [], $schema_name = 'chado') {
function chado_insert_cvterm($term, $options = [], $schema_name = NULL) {
// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Get the term properties.
$id = (isset($term['id'])) ? $term['id'] : '';
$name = '';
Expand Down
55 changes: 45 additions & 10 deletions tripal_chado/src/api/tripal_chado.db.api.php
View file
Original file line number Diff line number Diff line change
Expand Up @@ -65,14 +65,19 @@
*
* @ingroup tripal_chado_database_api
*/
function chado_get_db($identifiers, $options = [], $schema_name = 'chado') {
function chado_get_db($identifiers, $options = [], $schema_name = NULL) {

// Set Defaults.
// Set default options.
if (!isset($options['include_fk'])) {
// Tells chado_generate_var not to follow any foreign keys.
$options['include_fk'] = [];
}

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Error Checking of parameters.
if (!is_array($identifiers)) {
tripal_report_error(
Expand Down Expand Up @@ -147,7 +152,12 @@ function chado_get_db($identifiers, $options = [], $schema_name = 'chado') {
*
* @ingroup tripal_chado_database_api
*/
function chado_get_db_select_options($schema_name = 'chado') {
function chado_get_db_select_options($schema_name = NULL) {

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

$dbs = chado_query(
"SELECT db_id, name FROM {db} ORDER BY name",
Expand Down Expand Up @@ -223,14 +233,19 @@ function chado_get_db_select_options($schema_name = 'chado') {
*
* @ingroup tripal_chado_database_api
*/
function chado_get_dbxref($identifiers, $options = [], $schema_name = 'chado') {
function chado_get_dbxref($identifiers, $options = [], $schema_name = NULL) {

// Set Defaults.
// Set default options.
if (!isset($options['include_fk'])) {
// Tells chado_generate_var not only expand the db.
$options['include_fk'] = ['db_id' => TRUE];
}

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Error Checking of parameters.
if (!is_array($identifiers)) {
tripal_report_error('tripal_db_api', TRIPAL_ERROR,
Expand Down Expand Up @@ -316,9 +331,14 @@ function chado_get_dbxref($identifiers, $options = [], $schema_name = 'chado') {
*
* @ingroup tripal_chado_database_api
*/
function chado_get_dbxref_url($dbxref, $options = [], $schema_name = 'chado') {
function chado_get_dbxref_url($dbxref, $options = [], $schema_name = NULL) {
$final_url = '';

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Create the URL for the term.
if ($dbxref->db_id->urlprefix) {
$db_count = 0;
Expand Down Expand Up @@ -370,7 +390,12 @@ function chado_get_dbxref_url($dbxref, $options = [], $schema_name = 'chado') {
*
* @ingroup tripal_chado_database_api
*/
function chado_insert_db($values, $options = [], $schema_name = 'chado') {
function chado_insert_db($values, $options = [], $schema_name = NULL) {

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// Default Values.
$dbname = $values['name'];
Expand Down Expand Up @@ -438,7 +463,12 @@ function chado_insert_db($values, $options = [], $schema_name = 'chado') {
*
* @ingroup tripal_chado_database_api
*/
function chado_insert_dbxref($values, $options = [], $schema_name = 'chado') {
function chado_insert_dbxref($values, $options = [], $schema_name = NULL) {

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

$db_id = $values['db_id'];
$accession = $values['accession'];
Expand Down Expand Up @@ -502,13 +532,18 @@ function chado_insert_dbxref($values, $options = [], $schema_name = 'chado') {
*
* @ingroup tripal_chado_database_api
*/
function chado_associate_dbxref($basetable, $record_id, $dbxref, $options = [], $schema_name = 'chado') {
function chado_associate_dbxref($basetable, $record_id, $dbxref, $options = [], $schema_name = NULL) {
$linking_table = $basetable . '_dbxref';
$foreignkey_name = $basetable . '_id';

// Default Values.
// Set default options.
$options['insert_dbxref'] = (isset($options['insert_dbxref'])) ? $options['insert_dbxref'] : TRUE;

// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}

// If the dbxref_id is set then we know it already exists.
// Otherwise, select to check.
if (!isset($dbxref['dbxref_id'])) {
Expand Down

0 comments on commit 0e78c14

Please sign in to comment.