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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_db_get_db ($select_values) | |
| tripal_db_get_db_by_db_id ($db_id) | |
| tripal_db_get_db_by_name ($name) | |
| tripal_db_get_db_options () | |
| tripal_db_get_dbxref ($select_values) | |
| tripal_db_get_dbxref_by_accession ($accession, $db_id=0) | |
| tripal_db_add_db ($dbname, $description= '', $url= '', $urlprefix= '', $update=0) | |
| tripal_db_add_dbxref ($db_id, $accession, $version= '', $description= '') | |
| tripal_db_add_db | ( | $ | dbname, |
| $ | description = '', |
||
| $ | url = '', |
||
| $ | urlprefix = '', |
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| $ | update = 0 |
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| ) |
Adds a new database to the Chado DB table and returns the DB object.
| $dbname | The name of the database. This name is usually used as the prefix for CV term accessions |
| $description | Optional. A description of the database. By default no description is required. |
| $url | Optional. The URL for the database |
| $urlprefix | Optional. The URL that is to be used as a prefix when constructing a link to a database term |
| $update | Optional. Set this to '1' to force an update of the database if it already exists. The default is to not update. If the database exists then nothing is added. |
Definition at line 291 of file tripal_db.api.inc.
{
// build the values array for inserting/updating
$ins_values = array(
'name' => $dbname,
'description' => $description,
'url' => $url,
'urlprefix' => $urlprefix
);
// get the database record if it already exists
$sel_values = array('name' => $dbname);
$sel_options = array('statement_name' => 'sel_db_na');
$result = tripal_core_chado_select('db', array('*'), $sel_values, $sel_options);
// if it does not exists then add it
if (count($result) == 0) {
$ins_options = array('statement_name' => 'ins_db_nadeurur');
$success = tripal_core_chado_insert('db', $ins_values, $ins_options);
if (!$success) {
watchdog('tripal_db', "Cannot create db '$dbname'.", NULL, WATCHDOG_WARNING);
return 0;
}
$result = tripal_core_chado_select('db', array('*'), $sel_values, $sel_options);
}
// if it exists and update is enabled the do the update
elseif ($update) {
$upd_options = array('statement_name' => 'upd_db_nadeurur');
$success = tripal_core_chado_update('db', $sel_values, $ins_values, $upd_options);
if (!$success) {
watchdog('tripal_db', "Cannot update db '$dbname'.", NULL, WATCHDOG_WARNING);
return 0;
}
$result = tripal_core_chado_select('db', array('*'), $sel_values, $sel_options);
}
// return the database object
return $result[0];
}
| tripal_db_add_dbxref | ( | $ | db_id, |
| $ | accession, | ||
| $ | version = '', |
||
| $ | description = '' |
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| ) |
Definition at line 336 of file tripal_db.api.inc.
{
$ins_values = array(
'db_id' => $db_id,
'accession' => $accession,
'version' => $version,
'description' => $description
);
// check to see if the dbxref exists
$sel_values = array(
'db_id' => $db_id,
'accession' => $accession,
);
$sel_options = array('statement_name' => 'sel_dbxref_dbacve', 'is_duplicate' => 1);
$result = tripal_core_chado_select('dbxref', array('*'), $sel_values, $sel_options);
// if it doesn't already exist then add it
if (!$result) {
$ins_options = array('statement_name' => 'ins_dbxref_dbacvede');
$success = tripal_core_chado_insert('dbxref', $ins_values, $ins_options);
if (!$success) {
watchdog('tripal_cv', "Failed to insert the dbxref record $accession", NULL, WATCHDOG_WARNING);
return 0;
}
$result = tripal_core_chado_select('dbxref', array('*'), $sel_values, $sel_options);
}
return $result[0];
}
| tripal_db_get_db | ( | $ | select_values | ) |
Purpose: To retrieve a chado database object
| $select_values | An array meant to uniquely select a given database |
The database is selected using tripal_core_chado select and as such the $select_values array parameter meant to uniquely identify the database to be returned follows the same form as when using tripal_core_chado_select directly.
Example Usage:
$select_values = array(
'name' => 'SOFP'
);
$db_object = tripal_db_get_db($select_values);
The above code selects the SOFP db and returns the following object:
$db_object = stdClass Object (
[db_id] => 49
[name] => SOFP
[description] =>
[urlprefix] =>
[url] =>
);
Definition at line 44 of file tripal_db.api.inc.
{
$columns = array(
'db_id',
'name',
'description',
'urlprefix',
'url'
);
$results = tripal_core_chado_select('db', $columns, $select_values);
if (sizeof($results) == 1) {
return $results[0];
}
elseif (empty($results)) {
watchdog('tripal_cdb',
'tripal_db_get_db: No db matches criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
return FALSE;
}
else {
watchdog('tripal_db',
'tripal_db_get_db: 2+ dbs match criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
}
}
| tripal_db_get_db_by_db_id | ( | $ | db_id | ) |
Purpose: To retrieve a chado db object
| $db_id | db.db_id |
Definition at line 85 of file tripal_db.api.inc.
{
$r = db_fetch_object(chado_query(
"SELECT * FROM {db} WHERE db_id=%d", $db_id
));
return $r;
}
| tripal_db_get_db_by_name | ( | $ | name | ) |
Purpose: To retrieve a chado db object
| $name | db.name |
Definition at line 104 of file tripal_db.api.inc.
{
$r = db_fetch_object(chado_query(
"SELECT * FROM {db} WHERE name='%s'", $name
));
return $r;
}
| tripal_db_get_db_options | ( | ) |
Purpose: Create an options array to be used in a form element which provides a list of all chado dbs
Definition at line 135 of file tripal_db.api.inc.
{
$result = chado_query(
"SELECT db_id, name FROM {db}"
);
$options = array();
while ( $r = db_fetch_object($result) ) {
$options[$r->db_id] = $r->name;
}
return $options;
}
| tripal_db_get_dbxref | ( | $ | select_values | ) |
Purpose: To retrieve a chado database reference object
| $select_values | An array meant to uniquely select a given database reference |
The database reference is selected using tripal_core_chado select and as such the $select_values array parameter meant to uniquely identify the database reference to be returned follows the same form as when using tripal_core_chado_select directly.
Example Usage:
$select_values = array(
'accession' => 'synonym',
'db_id' => array(
'name' => 'SOFP'
)
);
$dbxref_object = tripal_db_get_dbxref($select_values);
The above code selects the synonym database reference and returns the following object:
$dbxref_object = stdClass Object (
[dbxref_id] => 2581
[accession] => synonym
[description] =>
[version] =>
[db_db_id] => 49
[db_name] => SOFP
[db_description] =>
[db_urlprefix] =>
[db_url] =>
);
Definition at line 203 of file tripal_db.api.inc.
{
$columns = array(
'dbxref_id',
'db_id',
'accession',
'description',
'version'
);
$results = tripal_core_chado_select('dbxref', $columns, $select_values);
if (sizeof($results) == 1) {
$dbxref = tripal_db_add_db_to_object(array('db_id' => $results[0]->db_id), $results[0], array());
unset($dbxref->db_id);
return $dbxref;
}
elseif (empty($results)) {
watchdog('tripal_db',
'tripal_db_get_dbxref: No dbxref matches criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
return FALSE;
}
else {
watchdog('tripal_db',
'tripal_db_get_dbxref: 2+ dbxrefs match criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
}
}
| tripal_db_get_dbxref_by_accession | ( | $ | accession, |
| $ | db_id = 0 |
||
| ) |
Purpose: To retrieve a chado dbxref object with a given accession
| $accession | dbxref.accession |
| $db_id | dbxref.db_id |
Definition at line 249 of file tripal_db.api.inc.
{
if (!empty($db_id)) {
$r = db_fetch_object(chado_query(
"SELECT * FROM {dbxref} WHERE accession='%s' AND db_id=%d",
$accession, $db_id
));
}
else {
$r = db_fetch_object(chado_query(
"SELECT * FROM {dbxref} WHERE accession='%s'",
$accession
));
}
return $r;
}
1.7.4