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Tripal v1.0 (6.x-1.0)
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Tripal v1.0 (6.x-1.0)
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Functions | |
| tripal_stock_get_stock_by_nid ($nid) | |
| tripal_stock_get_stock_by_stock_id ($stock_id) | |
| tripal_stock_get_all_stocks () | |
| tripal_stock_get_stocks ($values) | |
| tripal_stock_get_stocks_by_stockprop ($stockprop_values, $stock_values) | |
| tripal_stock_get_stock_by_name_identifier ($name, $organism_id) | |
| tripal_stock_get_all_stocks | ( | ) |
Purpose: Returns all stocks currently sync'd with drupal
Definition at line 60 of file tripal_stock.api.inc.
{
$sql = "SELECT stock_id, nid from {chado_stock}";
$resource = db_query($sql);
$stocks = array();
while ($r = db_fetch_object($resource)) {
$node = node_load($r->nid);
if ($node) {
$stocks[$r->stock_id] = $node;
}
}
return $stocks;
}
| tripal_stock_get_stock_by_name_identifier | ( | $ | name, |
| $ | organism_id | ||
| ) |
Purpose: Return all stocks with a given name identifier which might match stock.name, stock.uniquename, dbxref.accession, stockprop.value where stockprop.type='synonym'
| $name | The name identfier to be used |
| $organism_id | The stock.organism_id of the stock to be selected |
Definition at line 208 of file tripal_stock.api.inc.
{
$stock_ids = array();
$options = array(
'case_insensitive_columns' => array('name', 'uniquename', 'accession', 'value')
);
// where name_identifier = stock.name-------------------------------
$current_stocks = tripal_core_chado_select('stock', array('stock_id'),
array(
'name' => $name,
'organism_id' => $organism_id,
),
array(
'case_insensitive_columns' => array('name'),
)
);
if (!empty($current_stocks)) {
foreach ($current_stocks as $c) {
$stock_ids[] = $c->stock_id; }
}
// where name_identifier = stock.uniquename-------------------------------
$current_stocks = tripal_core_chado_select('stock', array('stock_id'),
array(
'uniquename' => $name,
'organism_id' => $organism_id,
),
array(
'case_insensitive_columns' => array('uniquename'),
)
);
if (!empty($current_stocks)) {
foreach ($current_stocks as $c) {
$stock_ids[] = $c->stock_id; }
}
// where name_identifier = dbxref.accession-------------------------------
// linked to stock through stock.dbxref
$current_stocks = tripal_core_chado_select('stock', array('stock_id'),
array(
'dbxref_id' => array(
'accession' => $name,
),
'organism_id' => $organism_id,
),
array(
'case_insensitive_columns' => array('accession'),
)
);
if (!empty($current_stocks)) {
foreach ($current_stocks as $c) {
$stock_ids[] = $c->stock_id; }
}
// linked to stock through stock_dbxref?
$current_stocks = tripal_core_chado_select('stock_dbxref', array('stock_id'),
array(
'dbxref_id' => array(
'accession' => $name,
),
'stock_id' => array(
'organism_id' => $organism_id,
),
),
array(
'case_insensitive_columns' => array('accession'),
)
);
if (!empty($current_stocks)) {
foreach ($current_stocks as $c) {
$stock_ids[] = $c->stock_id;
}
}
// where name_identifier = stockprop.value-------------------------------
// where type='synonym'
$current_stocks = tripal_core_chado_select('stockprop', array('stock_id'),
array(
'stock_id' => array(
'organism_id' => $organism_id,
),
'type_id' => array(
'cv_id' => variable_get('chado_stock_prop_types_cv', 'null'),
'name' => 'synonym',
),
'value' => $name,
),
array(
'case_insensitive_columns' => array('value'),
)
);
if (!empty($current_stocks)) {
foreach ($current_stocks as $c) {
$stock_ids[] = $c->stock_id;
}
}
// Change from stock_ids to nodes-----------------------------------
$stock_ids = array_filter($stock_ids);
$stock_ids = array_unique($stock_ids);
$stocks = array();
foreach ($stock_ids as $stock_id) {
$node = tripal_stock_get_stock_by_stock_id($stock_id);
if ($node) {
$stocks[] = $node;
}
}
return $stocks;
}
| tripal_stock_get_stock_by_nid | ( | $ | nid | ) |
Purpose: Return a given stock node using the nid
| $nid | The node ID of the stock you want to load |
Definition at line 23 of file tripal_stock.api.inc.
{
return node_load($nid);
}
| tripal_stock_get_stock_by_stock_id | ( | $ | stock_id | ) |
Purpose: Return a given stock object using the stock id
Definition at line 37 of file tripal_stock.api.inc.
{
$sql = "SELECT nid FROM {chado_stock} WHERE stock_id=%d";
$r = db_fetch_object(db_query($sql, $stock_id));
if (!empty($r->nid)) {
return node_load($r->nid);
}
else {
watchdog('tripal_stock', 'tripal_stock_get_stock_by_stock_id(!stock_id): no stock with that stock_id is sync\'d with drupal', array('!stock_id' => $stock_id), WATCHDOG_WARNING);
}
return 0;
}
| tripal_stock_get_stocks | ( | $ | values | ) |
Purpose: Return all stocks that match a given criteria
| $values | An associative array containing the values for filtering the results. |
Example usage:
$values = array(
'organism_id' => array(
'genus' => 'Lens',
'species' => 'culinaris',
),
'name' => 'CDC Redberry',
'type_id' => array (
'cv_id' => array (
'name' => 'germplasm',
),
'name' => 'registered_cultivar',
'is_obsolete' => 0
),
);
$result = tripal_stock_get_stocks($values);
The above code selects a record from the chado stock table using three fields with values which identify a stock or multiple stocks. Then the node for each stock identified is returned, if it exists. The $values array is nested such that the organism is identified by way of the organism_id foreign key constraint by specifying the genus and species. The cvterm is also specified using its foreign key and the cv_id for the cvterm is nested as well.
Definition at line 109 of file tripal_stock.api.inc.
{
$stock_ids = tripal_core_chado_select('stock', array('stock_id'), $values);
// Change from stock_ids to nodes-----------------------------------
$stock_ids = array_filter($stock_ids);
$stock_ids = array_unique($stock_ids);
$stocks = array();
foreach ($stock_ids as $stock_id) {
$node = tripal_stock_get_stock_by_stock_id($stock_id->stock_id);
if ($node) {
$stocks[] = $node;
}
}
return $stocks;
}
| tripal_stock_get_stocks_by_stockprop | ( | $ | stockprop_values, |
| $ | stock_values | ||
| ) |
Purpose: Retrieve stocks based on associated stock properties
| $stockprop_values | An array of column_name => value where column_name is any column in the stockprop table and value is the value you want that column to be. This is used as a tripal_core_chado_select values array so nesting is allowed. |
| $stock_values | An array of column_name => value where column_name is any column in the stock table and value is the value you want that column to be. This is used as a tripal_core_chado_select values array so nesting is allowed. |
Example usage:
$stockprop_values = array(
'value' => 'CDC Redberry',
'type_id' => array (
'cv_id' => array (
'name' => 'stock_properties',
),
'name' => 'synonym',
'is_obsolete' => 0
),
);
$stock_values = array(
'organism_id' => array(
'genus' => 'Lens',
'species' => 'culinaris',
),
);
$result = tripal_stock_get_stocks_by_stockprop($stockprop_values, $stock_values);
The above code selects all Lens culinaris stocks with the synonym (stock property) CDC Redberry. The nodes for each stock selected are loaded and returned in an array.
Definition at line 168 of file tripal_stock.api.inc.
{
//add stock values to stockprop values
if (!empty($stock_values)) {
$stockprop_values['stock_id'] = $stock_values;
}
//get stock_ids from stockprop table
$stock_ids = tripal_core_chado_select('stockprop', array('stock_id'), $stockprop_values);
// Change from stock_ids to nodes-----------------------------------
$stock_ids = array_filter($stock_ids);
$stock_ids = array_unique($stock_ids);
$stocks = array();
foreach ($stock_ids as $stock_id) {
$node = tripal_stock_get_stock_by_stock_id($stock_id->stock_id);
if ($node) {
$stocks[] = $node;
}
}
return $stocks;
}
1.7.4