tripal_chado/src/api/tripal_chado.cv.api.php
<?php
/**
* @file
* Provides API functions specifically for managing controlled vocabulary
* records in Chado.
*
* @ingroup tripal_chado
*/
/**
* @defgroup tripal_chado_cv_api Chado CV
* @ingroup tripal_chado_api
* @{
* Provides API functions specifically for managing controlled vocabulary
* records in Chado. Please note that Tripal v3 provides a generic set of
* API functions for working with controlled vocabularies (CVs). This allows for
* CVs to be stored using any back-end. By default CV's continue to be housed
* in Chado. Therefore, if you are working directly with controlled vocabulary
* records inside of a Chado-aware module then these functions can be used.
* @}
*/
/**
* Retrieves a chado controlled vocabulary variable
*
* @param $identifier
* An array with the key stating what the identifier is. Supported keys (only
* on of the following unique keys is required):
* - cv_id: the chado cv.cv_id primary key.
* - name: the chado cv.name field (assume unique).
* @param $options
* An array of options. Supported keys include:
* - Any keys supported by chado_generate_var(). See that function
* definition fot additional details.
* @param $schema_name
* The name of the chado schema the records reside in.
*
* NOTE: the $identifier parameter can really be any array similar to $values
* passed into chado_select_record(). It should fully specify the cv record to
* be returned.
*
* @return
* If unique values were passed in as an identifier then an object describing
* the cv will be returned (will be a chado variable from
* chado_generate_var()). Otherwise, FALSE will be returned.
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cv($identifiers, $options = [], $schema_name = NULL) {
// Set default options.
if (!isset($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(
'tripal_chado_api',
TRIPAL_ERROR,
"chado_get_cv: The identifier passed in is expected to be an array with the key
matching a column name in the cv table (ie: cv_id or name). You passed in %identifier.",
[
'%identifier' => print_r($identifiers, TRUE),
]
);
}
elseif (empty($identifiers)) {
tripal_report_error(
'tripal_chado_api',
TRIPAL_ERROR,
"chado_get_cv: You did not pass in anything to identify the cv you want. The identifier
is expected to be an array with the key matching a column name in the cv table
(ie: cv_id or name). You passed in %identifier.",
[
'%identifier' => print_r($identifiers, TRUE),
]
);
}
// Try to get the cv.
$cv = chado_generate_var(
'cv',
$identifiers,
$options,
$schema_name
);
// Ensure the cv is singular. If it's an array then it is not singular.
if (is_array($cv)) {
tripal_report_error(
'tripal_chado_api',
TRIPAL_ERROR,
"chado_get_cv: The identifiers you passed in were not unique. You passed in %identifier.",
[
'%identifier' => print_r($identifiers, TRUE),
]
);
}
// Report an error if $cv is FALSE since then chado_generate_var has failed.
elseif ($cv === FALSE) {
tripal_report_error(
'tripal_chado_api',
TRIPAL_ERROR,
"chado_get_cv: chado_generate_var() failed to return a cv based on the identifiers
you passed in. You should check that your identifiers are correct, as well as, look
for a chado_generate_var error for additional clues. You passed in %identifier.",
[
'%identifier' => print_r($identifiers, TRUE),
]
);
}
// Else, as far we know, everything is fine so give them their cv :)
else {
return $cv;
}
}
/**
* Create an options array to be used in a form element which provides a
* list of all chado cvs.
*
* @param $schema_name
* The name of the chado schema the records reside in.
*
* @return
* An array(cv_id => name) for each cv in the chado cv table.
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cv_select_options($schema_name = NULL) {
// Set default schema.
if (!$schema_name) {
$schema_name = \Drupal::config('tripal_chado.settings')->get('default_schema');
}
$results = chado_select_record(
'cv',
[
'cv_id',
'name',
],
[],
['order_by' => ['name' => 'ASC']],
$schema_name);
$options = [];
$options[] = 'Select a Vocabulary';
foreach ($results as $r) {
$options[$r->cv_id] = $r->name;
}
return $options;
}
/**
* Retrieves a chado controlled vocabulary term variable.
*
* @param $identifier
* An array apropriate for use with the chado_generate_var for uniquely
* identifying a cvterm record. Alternativley, there are also some specially
* handled keys. They are:
* - id: an ID for the term of the for [dbname]:[accession], where [dbname]
* is the short name of the vocabulary and accession is the unique ID.
* - cv_id: an integer indicating the cv_id or an array with 'name' => the
* name of the cv.
* - synonym: an array with 'name' => the name of the synonym of the cvterm
* you want returned; 'cv_id' => the cv_id of the synonym; 'cv_name' =>
* the name of the cv of the synonym.
* - property: An array/object describing the property to select records
* for. It should at least have either a type_name (if unique across cvs)
* or type_id. Other supported keys include: cv_id/cv_name (of the type),
* value and rank.
* @param $options
* An array of options. Supported keys include:
* - Any keys supported by chado_generate_var(). See that function
* definition for additional details.
* @param $schema_name
* The name of the chado schema the records reside in.
*
* NOTE: the $identifier parameter can really be any array similar to $values
* passed into chado_select_record(). It should fully specify the cvterm
* record to be returned.
*
* @return
* If unique values were passed in as an identifier then an object describing
* the cvterm will be returned (will be a chado variable from
* chado_generate_var()). Otherwise, FALSE will be returned.
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cvterm($identifiers, $options = [], $schema_name = NULL) {
// Set default options.
if (!isset($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,
"chado_get_cvterm: The identifier passed in is expected to be an array with the key
matching a column name in the cvterm table (ie: cvterm_id or name). You passed in %identifier.",
['%identifier' => print_r($identifiers, TRUE)]
);
}
elseif (empty($identifiers)) {
tripal_report_error('tripal_cv_api', TRIPAL_ERROR,
"chado_get_cvterm: You did not pass in anything to identify the cvterm you want. The identifier
is expected to be an array with the key matching a column name in the cvterm table
(ie: cvterm_id or name). You passed in %identifier.",
['%identifier' => print_r($identifiers, TRUE)]
);
}
// If synonym was passed in, then process this first before calling
// chado_generate_var().
if (isset($identifiers['synonym'])) {
$synonym = $identifiers['synonym']['name'];
$values = ['synonym' => $synonym];
if (isset($identifiers['synonym']['cv_id'])) {
$values['cvterm_id'] = ['cv_id' => $identifiers['synonym']['cv_id']];
}
if (isset($identifiers['synonym']['cv_name'])) {
$values['cvterm_id'] = ['cv_id' => ['name' => $identifiers['synonym']['cv_name']]];
}
$options = [
'case_insensitive_columns' => ['name'],
];
$result = chado_select_record('cvtermsynonym', ['cvterm_id'], $values, $options, $schema_name);
// if the synonym doens't exist or more than one record is returned then
// return false.
if (count($result) == 0) {
return FALSE;
}
if (count($result) > 1) {
return FALSE;
}
$identifiers = ['cvterm_id' => $result[0]->cvterm_id];
}
// If one of the identifiers is property then use chado_get_record_with_property().
if (isset($identifiers['property'])) {
$property = $identifiers['property'];
unset($identifiers['property']);
$cvterm = chado_get_record_with_property(
['table' => 'cvterm', 'base_records' => $identifiers],
['type_name' => $property],
$options
);
}
if (isset($identifiers['id'])) {
list($db_name, $accession) = preg_split('/:/', $identifiers['id']);
$cvterm = chado_generate_var(
'cvterm',
[
'dbxref_id' => [
'db_id' => [
'name' => $db_name,
],
'accession' => $accession,
],
],
[],
$schema_name
);
}
// Else we have a simple case and we can just use chado_generate_var to get
// the cvterm.
else {
// Try to get the cvterm.
$cvterm = chado_generate_var('cvterm', $identifiers, $options, $schema_name);
}
// Ensure the cvterm is singular. If it's an array then it is not singular.
if (is_array($cvterm)) {
tripal_report_error(
'tripal_cv_api',
TRIPAL_ERROR,
"chado_get_cvterm: The identifiers you passed in were not unique. You passed in %identifier.",
[
'%identifier' => print_r($identifiers, TRUE),
]
);
}
// Report an error if $cvterm is FALSE since then chado_generate_var has
// failed.
elseif ($cvterm === FALSE) {
tripal_report_error(
'tripal_cv_api',
TRIPAL_ERROR,
"chado_get_cvterm: chado_generate_var() failed to return a cvterm based on the identifiers
you passed in. You should check that your identifiers are correct, as well as, look
for a chado_generate_var error for additional clues. You passed in %identifier.",
[
'%identifier' => print_r($identifiers, TRUE),
]
);
}
// Else, as far we know, everything is fine so give them their cvterm :)
else {
return $cvterm;
}
}
/**
* Create an options array to be used in a form element
* which provides a list of all chado cvterms.
*
* @param $cv_id
* The chado cv_id; only cvterms with the supplied cv_id will be returnedl.
* @param $rel_type
* Set to TRUE if the terms returned should only be relationship types in
* the vocabulary. This is useful for creating drop-downs of terms
* used for relationship linker tables.
* @param $schema_name
* The name of the chado schema the records reside in.
*
* @return
* An associative array with the cvterm_id's as keys. The first
* element in the array has a key of '0' and a value of 'Select a Type'.
*
* @ingroup tripal_chado_cv_api
*/
function chado_get_cvterm_select_options($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) {
$values['is_relationshiptype'] = 1;
}
$s_options = ['order_by' => ['name' => 'ASC']];
$cvterms = chado_select_record('cvterm', $columns, $values, $s_options, $schema_name);
$options = [];
$options[0] = 'Select a Type';
foreach ($cvterms as $cvterm) {
$options[$cvterm->cvterm_id] = $cvterm->name;
}
return $options;
}
/**
* Adds a controlled vocabulary to the CV table of Chado.
*
* @param $name
* The name of the controlled vocabulary. These are typically all lower case
* with no special characters other than an undrescore (for spaces).
* @param $comment
* A description or definition of the vocabulary.
* @param $options
* No options currently supported. For consistency.
* @param $schema_name
* The name of the chado schema the records reside in.
*
* @return
* An object populated with fields from the newly added database.
*
* @ingroup tripal_chado_cv_api
*/
function chado_insert_cv($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 = [
'name' => $name,
'definition' => $definition,
];
// See if the CV default exists already in the database.
$sel_values = ['name' => $name];
$results = chado_select_record('cv', ['*'], $sel_values, [], $schema_name);
// If it does not exist then add it.
if (count($results) == 0) {
$success = chado_insert_record('cv', $ins_values, [], $schema_name);
if (!$success) {
tripal_report_error('tripal_chado', TRIPAL_WARNING, "Failed to create the CV record", []);
return FALSE;
}
$results = chado_select_record('cv', ['*'], $sel_values, [], $schema_name);
}
// If it already exists then do an update.
else {
$success = chado_update_record('cv', $sel_values, $ins_values, [], $schema_name);
if (!$success) {
tripal_report_error('tripal_chado', TRIPAL_WARNING, "Failed to update the CV record", []);
return FALSE;
}
$results = chado_select_record('cv', ['*'], $sel_values, [], $schema_name);
}
// Return the cv object.
return $results[0];
}
/**
* Add's a controlled vocabulary term to Chado.
*
* This function will add a cvterm record (and a dbxref record if appropriate
* values are provided). If the parent vocabulary does not exist then
* that also is added to the cv table. If the cvterm is a relationship term
* then the 'is_relationship' value should be set. All
* terms must also have a corresponding database. This is specified in the
* term's ID just before the colon (e.g. GO:003824). If the database does not
* exist in the DB table then it will be added automatically. The accession
* (the value just after the colon in the term's ID) will be added to the
* dbxref table. If the CVterm already exists and $update is set (default)
* then the cvterm is updated. If the CVTerm already exists and $update is
* not set, then no changes are made and the CVTerm object is returned.
*
* @param $term
* An associative array with the following keys:
* - id: the term accession. must be of the form <DB>:<ACCESSION>, where
* <DB> is the name of the database to which the cvterm belongs and the
* <ACCESSION> is the term's accession number in the database.
* - name: the name of the term. usually meant to be human-readable.
* - is_obsolete: is present and set to 1 if the term is defunct.
* - definition: the definition of the term.
* - cv_name: The CV name to which the term belongs. If this arugment is
* null or not provided then the function tries to find a record in the
* CV table with the same name provided in the $term[namespace]. If
* this field is provided then it overrides what the value in
* $term[namespace].
* - is_relationship: If this term is a relationship term then this value
* should be 1.
* - db_name: In some cases the database name will not be part of the
* $term['id'] and it needs to be explicitly set. Use this argument
* only if the database name cannot be specififed in the term ID
* (e.g. <DB>:<ACCESSION>).
* @param $options
* An associative array with the following keys:
* - update_existing: By default this is TRUE. If the term exists it is
* automatically updated.
* @param $schema_name
* The name of the chado schema the records reside in.
*
* @return
* A cvterm object
*
* @ingroup tripal_chado_cv_api
*/
function chado_insert_cvterm($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 = '';
$cvname = '';
$definition = '';
$is_obsolete = 0;
$accession = '';
// Set Defaults.
if (isset($term['cv_name'])) {
$cvname = $term['cv_name'];
}
else {
$cvname = 'local';
}
// Namespace is deprecated but must be supported for backwards
// compatability.
if (array_key_exists('namespace', $term)) {
$cvname = $term['namespace'];
}
$is_relationship = 0; // default value
if (isset($term['is_relationship'])) {
$is_relationship = $term['is_relationship'];
}
$dbname = 'internal'; // default value
if (isset($term['db_name'])) {
$dbname = $term['db_name'];
}
$update = 1; // default value
if (isset($options['update_existing'])) {
$update = $options['update_existing'];
}
$name = $id; // default value
if (array_key_exists('name', $term)) {
$name = $term['name'];
}
$definition = ''; //default value
if (array_key_exists('definition', $term)) {
$definition = preg_replace('/^\"(.*)\"/', '\1', $term['definition']);
}
if (array_key_exists('is_obsolete', $term)) {
$is_obsolete = $term['is_obsolete'];
if (strcmp($is_obsolete, 'true') == 0) {
$is_obsolete = 1;
}
}
if (!$name and !$id) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find cvterm without 'id' or 'name'", []);
return 0;
}
if (!$id) {
$id = $name;
}
// Get the accession and the database from the cvterm id.
if ($dbname) {
$accession = $id;
}
if (preg_match('/^.+?:.*$/', $id)) {
$accession = preg_replace('/^.+?:(.*)$/', '\1', $id);
$dbname = preg_replace('/^(.+?):.*$/', '\1', $id);
}
// Check that we have a database name, give a different message if it's a
// relationship.
if ($is_relationship and !$dbname) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "A database name is not provided for this relationship term: $id", []);
return 0;
}
if (!$is_relationship and !$dbname) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "A database identifier is missing from the term: $id", []);
return 0;
}
// Check if CV already exists
//$cv = chado_get_cv(['name' => $cvname], [], $schema_name); // BEFOREOPT: 5.9ms
// OPT: 5.3ms
$sql_cv = "SELECT cv_id FROM {cv} WHERE name = :name LIMIT 1";
$results_cv = chado_query($sql_cv, [':name' => $cvname], [], $schema_name);
$cv = null;
foreach ($results_cv as $row_cv) {
$cv = new stdClass();
$cv->cv_id = $row_cv->cv_id;
}
// If CV does not exist
if (!$cv) {
$cv = chado_insert_cv($cvname, '', [], $schema_name);
}
if (!$cv) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find namespace '$cvname' when adding/updating $id", []);
return 0;
}
// This SQL statement will be used a lot to find a cvterm so just set it
// here for easy reference below. Because CV terms can change their names
// but accessions don't change, the following SQL finds cvterms based on
// their accession rather than the name.
$cvtermsql = "
SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname,
DB.name as dbname, DB.db_id, DBX.accession
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
INNER JOIN {db} DB on DBX.db_id = DB.db_id
INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
WHERE DBX.accession = :accession and DB.name = :name
";
// Add the database. The function will just return the DB object if the
// database already exists.
$db = chado_get_db(['name' => $dbname], [], $schema_name);
if (!$db) {
$db = chado_insert_db(['name' => $dbname], [], $schema_name);
}
if (!$db) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Cannot find database '$dbname' in Chado.", []);
return 0;
}
// The cvterm table has two unique dependencies. We need to check both.
// first check the (name, cv_id, is_obsolete) constraint.
$values = [
'name' => $name,
'is_obsolete' => $is_obsolete,
'cv_id' => [
'name' => $cvname,
],
];
$result = chado_select_record('cvterm', ['*'], $values, [], $schema_name);
if (count($result) == 1) {
$cvterm = $result[0];
// Get the dbxref record.
$values = ['dbxref_id' => $cvterm->dbxref_id];
$result = chado_select_record('dbxref', ['*'], $values, [], $schema_name);
$dbxref = $result[0];
if (!$dbxref) {
tripal_report_error('tripal_cv', TRIPAL_ERROR,
'Unable to access the dbxref record for the :term cvterm. Term Record: !record',
[':term' => $name, '!record' => print_r($cvterm, TRUE)]
);
return FALSE;
}
// Get the db.
$values = ['db_id' => $dbxref->db_id];
$result = chado_select_record('db', ['*'], $values, [], $schema_name);
$db_check = $result[0];
// // The database name for this existing term does not match that of the
// // one provided to this function. The CV name matches otherwise we
// // wouldn't have made it this far. So, let's swap the database for
// // this term.
// if ($db_check->name != $db->name) {
// // Look to see if the correct dbxref record already exists for this
// // database.
// $values = array(
// 'db_id' => $db->db_id,
// 'accession' => $accession,
// );
// $result = chado_select_record('dbxref', array('*'), $values);
// // If we already have a good dbxref then we want to update our cvterm
// // to use this dbxref.
// if (count($result) > 0) {
// $dbxref = $result[0];
// $match = array('cvterm_id' => $cvterm->cvterm_id);
// $values = array('dbxref_id' => $dbxref->dbxref_id);
// $success = chado_update_record('cvterm', $match, $values);
// if (!$success) {
// tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to correct the dbxref id for the cvterm " .
// "'$name' (id: $accession), for database $dbname", NULL);
// return 0;
// }
// }
// // If we don't have the dbxref then we want to delete our cvterm and let
// // the code below recreate it with the correct info.
// else {
// $match = array('cvterm_id' => $cvterm->cvterm_id);
// chado_delete_record('cvterm', $match);
// }
// }
// Check that the accession matches. Sometimes an OBO can define a term
// multiple times but with different accessions. If this is the case we
// can't do an insert or it will violate the constraint in the cvterm table.
// So we'll need to add the record to the cvterm_dbxref table instead.
if ($dbxref->accession != $accession) {
// Get/add the dbxref for his term.
$dbxref_new = chado_insert_dbxref([
'db_id' => $db->db_id,
'accession' => $accession,
], [], $schema_name);
if (!$dbxref_new) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
"$name (id: $accession), for database $dbname", []);
return 0;
}
// Check to see if the cvterm_dbxref record already exists.
$values = [
'cvterm_id' => $cvterm->cvterm_id,
'dbxref_id' => $dbxref_new->dbxref_id,
'is_for_definition' => 1,
];
$result = chado_select_record('cvterm_dbxref', ['*'], $values, [], $schema_name);
// if the cvterm_dbxref record does not exist then add it
if (count($result) == 0) {
$options = [
'return_record' => FALSE,
];
$success = chado_insert_record('cvterm_dbxref', $values, $options, $schema_name);
if (!$success) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the cvterm_dbxref record for a " .
"duplicated cvterm: $name (id: $accession), for database $dbname", []);
return 0;
}
}
// Get the original cvterm with the same name and return that.
$result = chado_query($cvtermsql, [
':accession' => $dbxref->accession,
':name' => $dbname,
], [], $schema_name);
$cvterm = $result->fetchObject();
return $cvterm;
}
// Continue on, we've fixed the record if the db_id did not match.
// We can now perform and updated if we need to.
}
// Get the CVterm record.
$result = chado_query($cvtermsql, [
':accession' => $accession,
':name' => $dbname,
], [], $schema_name);
$cvterm = $result->fetchObject();
if (!$cvterm) {
// Check to see if the dbxref exists if not, add it.
$dbxref = chado_insert_dbxref([
'db_id' => $db->db_id,
'accession' => $accession,
], [], $schema_name);
if (!$dbxref) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
"$name (id: $accession), for database $dbname", []);
return 0;
}
// Check to see if the dbxref already has an entry in the cvterm table.
$values = ['dbxref_id' => $dbxref->dbxref_id];
$check = chado_select_record('cvterm', ['cvterm_id'], $values, [], $schema_name);
if (count($check) == 0) {
// now add the cvterm
$ins_values = [
'cv_id' => $cv->cv_id,
'name' => $name,
'definition' => $definition,
'dbxref_id' => $dbxref->dbxref_id,
'is_obsolete' => $is_obsolete,
'is_relationshiptype' => $is_relationship,
];
$success = chado_insert_record('cvterm', $ins_values, [], $schema_name);
if (!$success) {
if (!$is_relationship) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the term: $name ($dbname)", []);
return 0;
}
else {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)", []);
return 0;
}
}
}
// This dbxref already exists in the cvterm table.
else {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", []);
return 0;
}
$result = chado_query($cvtermsql, [
':accession' => $accession,
':name' => $dbname,
], [], $schema_name);
$cvterm = $result->fetchObject();
}
// Update the cvterm.
elseif ($update) {
// First, basic update of the term.
$match = ['cvterm_id' => $cvterm->cvterm_id];
$upd_values = [
'name' => $name,
'definition' => $definition,
'is_obsolete' => $is_obsolete,
'is_relationshiptype' => $is_relationship,
];
$success = chado_update_record('cvterm', $match, $upd_values, [], $schema_name);
if (!$success) {
tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to update the term: $name", []);
return 0;
}
// Second, check that the dbxref has not changed and if it has then update
// it.
$checksql = "
SELECT cvterm_id
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
INNER JOIN {db} DB on DBX.db_id = DB.db_id
INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
WHERE DBX.accession = :accession and DB.name = :dbname and CVT.name = :term and CV.name = :cvname
";
$check = chado_query($checksql, [
':accession' => $accession,
':dbname' => $dbname,
':term' => $name,
':cvname' => $cvname,
], [], $schema_name)->fetchObject();
if (!$check) {
// Check to see if the dbxref exists if not, add it.
$dbxref = chado_insert_dbxref([
'db_id' => $db->db_id,
'accession' => $accession,
], [], $schema_name);
if (!$dbxref) {
tripal_report_error('tripal_chado', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
"$name (id: $accession), for database $dbname", []);
return 0;
}
$match = ['cvterm_id' => $cvterm->cvterm_id];
$upd_values = [
'dbxref_id' => $dbxref->dbxref_id,
];
$success = chado_update_record('cvterm', $match, $upd_values, [], $schema_name);
if (!$success) {
tripal_report_error('tripal_chado', TRIPAL_WARNING, "Failed to update the term $name with new accession $db:$accession", []);
return 0;
}
}
// Finally grab the updated details.
$result = chado_query($cvtermsql, [
':accession' => $accession,
':name' => $dbname,
], [], $schema_name);
$cvterm = $result->fetchObject();
}
else {
// Do nothing, we have the cvterm but we don't want to update.
}
// Return the cvterm.
return $cvterm;
}
/**
* This function is intended to be used in autocomplete forms.
*
* This function searches for a matching controlled vobulary name.
*
* @param $string
* The string to search for.
*
* @return
* A json array of terms that begin with the provided string.
*
* @ingroup tripal_chado_cv_api
*/
function chado_autocomplete_cv($string = '') {
$sql = "
SELECT CV.cv_id, CV.name
FROM {cv} CV
WHERE lower(CV.name) like lower(:name)
ORDER by CV.name
LIMIT 25 OFFSET 0
";
$results = chado_query($sql, [':name' => $string . '%']);
$items = [];
foreach ($results as $cv) {
$items[$cv->name] = $cv->name;
}
drupal_json_output($items);
}
/**
* This function is intended to be used in autocomplete forms
* for searching for CV terms that begin with the provided string.
*
* @param $cv_id
* The CV ID in which to search for the term.
* @param $string
* The string to search for.
*
* @return
* A json array of terms that begin with the provided string.
*
* @ingroup tripal_chado_cv_api
*/
function chado_autocomplete_cvterm($cv_id, $string = '') {
if ($cv_id) {
$sql = "
SELECT CVT.cvterm_id, CVT.name
FROM {cvterm} CVT
WHERE CVT.cv_id = :cv_id and lower(CVT.name) like lower(:name)
UNION
SELECT CVT2.cvterm_id, CVTS.synonym as name
FROM {cvterm} CVT2
INNER JOIN {cvtermsynonym} CVTS ON CVTS.cvterm_id = CVT2.cvterm_id
WHERE CVT2.cv_id = :cv_id and lower(CVTS.synonym) like lower(:name)
ORDER by name
LIMIT 25 OFFSET 0
";
$results = chado_query($sql, [
':cv_id' => $cv_id,
':name' => $string . '%',
]);
$items = [];
foreach ($results as $term) {
$items[$term->name] = $term->name;
}
}
// If a CV wasn't provided then search all of them, and include the cv
// in the results.
else {
$sql = "
SELECT CVT.cvterm_id, CVT.name, CV.name as cvname, CVT.cv_id
FROM {cvterm} CVT
INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
WHERE lower(CVT.name) like lower(:name)
UNION
SELECT CVT2.cvterm_id, CVTS.synonym as name, CV2.name as cvname, CVT2.cv_id
FROM {cvterm} CVT2
INNER JOIN {cv} CV2 on CVT2.cv_id = CV2.cv_id
INNER JOIN {cvtermsynonym} CVTS ON CVTS.cvterm_id = CVT2.cvterm_id
WHERE lower(CVTS.synonym) like lower(:name)
ORDER by name
LIMIT 25 OFFSET 0
";
$results = chado_query($sql, [':name' => $string . '%']);
$items = [];
foreach ($results as $term) {
$items[$term->name] = $term->name;
}
}
drupal_json_output($items);
}
/**
* Add a record to a cvterm linking table (ie: feature_cvterm).
*
* @param $basetable
* The base table to which the cvterm should be linked/associated. Thus to
* associate a cvterm to a feature the basetable=feature and cvterm_id is
* added to the feature_cvterm table.
* @param $record_id
* The primary key of the basetable to associate the cvterm with. This should
* be in integer.
* @param $cvterm
* An associative array describing the cvterm. Valid keys include:
* - name: the name for the cvterm,
* - cv_name: the name of the cv the cvterm belongs to.
* - cv_id: the primary key of the cv the cvterm belongs to.
* @param $options
* An associative array of options. Valid keys include:
* - insert_cvterm: Insert the cvterm if it doesn't already exist. FALSE is
* the default.
* @param $schema_name
* The name of the chado schema the record resides in.
*
* @ingroup tripal_chado_cv_api
*/
function chado_associate_cvterm($basetable, $record_id, $cvterm, $options, $schema_name) {
$linking_table = $basetable . '_cvterm';
$foreignkey_name = $basetable . '_id';
// Default Values
$options['insert_cvterm'] = (isset($options['insert_cvterm'])) ? $options['insert_cvterm'] : FALSE;
// If the cvterm_id is not set then find the cvterm record using the name and
// cv_id.
if (!isset($cvterm['cvterm_id'])) {
$values = [
'name' => $cvterm['name'],
];
if (isset($cvterm['cv_id'])) {
$values['cv_id'] = $cvterm['cv_id'];
}
elseif (isset($cvterm['cv_name'])) {
$values['cv_id'] = [
'name' => $cvterm['cv_name'],
];
}
else {
tripal_report_error('tripal_chado_api', TRIPAL_WARNING,
"chado_associate_cvterm: The cvterm needs to have either the cv_name or cv_id
supplied. You were trying to associate a cvterm with the %base %record_id
and supplied the cvterm values: %cvterm.",
[
'%base' => $basetable,
'%record_id' => $record_id,
'%cvterm' => print_r($cvterm, TRUE),
]
);
print "need cv_id/cv_name:" . print_r($values, TRUE);
return FALSE;
}
// Get the cvterm. If it doesn't exist then add it if the option
// 'insert_cvterm' is set.
$select = chado_select_record('cvterm', ['*'], $values, [], $schema_name);
if ($select) {
$cvterm['cvterm_id'] = $select[0]->cvterm_id;
}
elseif ($options['insert_cvterm']) {
// Insert the cvterm
$insert = chado_insert_cvterm($values, [], $schema_name);
if (isset($insert->cvterm_id)) {
$cvterm['cvterm_id'] = $insert->cvterm_id;
}
else {
tripal_report_error('tripal_chado_api', TRIPAL_WARNING,
"chado_associate_cvterm: Unable to insert the cvterm using the cvterm values: %cvterm.",
['%cvterm' => print_r($cvterm, TRUE)]
);
print "Unable to insert cvterm:" . print_r($values, TRUE);
return FALSE;
}
}
else {
tripal_report_error('tripal_api', TRIPAL_WARNING,
"chado_associate_cvterm: The cvterm doesn't already exist. You supplied the cvterm values: %cvterm.",
['%cvterm' => print_r($cvterm, TRUE)]
);
print "Cvterm doesn't already exist:" . print_r($values, TRUE);
return FALSE;
}
}
// Now add the link between the record & cvterm.
if ($cvterm['cvterm_id'] > 0) {
$values = [
'cvterm_id' => $cvterm['cvterm_id'],
$foreignkey_name => $record_id,
'pub_id' => 1,
];
// Check if the cvterm is already associated. If so, don't re-add it.
$result = chado_select_record($linking_table, ['*'], $values, [], $schema_name);
if (!$result) {
$success = chado_insert_record($linking_table, $values, [], $schema_name);
if (!$success) {
tripal_report_error('tripal_api', TRIPAL_WARNING,
"Failed to insert the %base record %term",
['%base' => $linking_table, '%term' => $cvterm['name']]
);
print "Unable to insert linking record:" . print_r($values, TRUE);
return FALSE;
}
$result = chado_select_record($linking_table, ['*'], $values, [], $schema_name);
}
if (isset($result[0])) {
return $result[0];
}
else {
print "2nd last:" . print_r($values, TRUE);
return FALSE;
}
}
print "last:" . print_r($values, TRUE);
return FALSE;
}