<?php
/**
* @file
* Controlled Vocabulary API
*
* @defgroup tripal_cv_api CV Module API
* @ingroup tripal_api
* This module provides a set of functions to simplify working with
* controlled vocabularies. Most of the API functions deal with retrieving
* terms or their parent vocabularies.
*
* However, the API also supports
* generation of trees for browsing a vocabulary as well as generation of
* pie graphs for display of hierarchical counts of terms. Version 0.3b of
* Tripal provides a feature browser and a feature summary chart uses
* the API functions provided here. But in general charts and trees can be
* created for any controlled vocabulary.
*
*/
/**
* Purpose: To retrieve a chado controlled vocabulary object
*
* @param $select_values
* An array meant to uniquely select a given controlled vocabulary
*
* @return
* Chado controlled vocabulary object
*
* The controlled vocabulary is selected using tripal_core_chado select and as such the
* $select_values array parameter meant to uniquely identify the controlled vocab to be
* returned follows the same form as when using tripal_core_chado_select directly.
*
* Example Usage:
* @code
$select_values = array(
'name' => 'feature_property'
);
$cv_object = tripal_cv_get_cv($select_values);
* @endcode
* The above code selects the feature_property cv and returns the following object:
* @code
$cv_object = stdClass Object (
[cv_id] => 13
[name] => feature_property
[definition] =>
);
* @endcode
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cv($select_values) {
$columns = array(
'cv_id',
'name',
'definition',
);
$results = tripal_core_chado_select('cv', $columns, $select_values);
if (sizeof($results) == 1) {
return $results[0];
}
elseif (empty($results)) {
watchdog('tripal_cv',
'tripal_cv_get_cv: No cv matches criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
return FALSE;
}
else {
watchdog('tripal_cv',
'tripal_cv_get_cv: 2+ cvs match criteria values:%values',
array('%values' => print_r($select_values, TRUE)),
WATCHDOG_WARNING
);
}
}
// Purpose: To retrieve a chado cv object
// @param $where_options
// @code
// array(
// <column_name> => array(
// 'type' => <type of column: INT/STRING>,
// 'value' => <the vlaue you want to filter on>,
// 'exact' => <if TRUE use =; if FALSE use ~>,
// )
// )
// @endcode
//
// @return
// Chado cv object with all fields from the chado cv table
//
// @ingroup tripal_cv_api
//
//function tripal_cv_get_cv ($where_options)
/**
* Retrieve a cv given the cv name
*
* @param $name
* The name of the cv to be returned
* @return
* The cv object for the specified CV name
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cv_by_name($name) {
$r = tripal_core_chado_select('cv', array('*'), array('name' => $name));
return $r[0];
}
/**
* Retrieve the cv object for the specified CV id
*
* NOTE: This function is deprecated.
* @see tripal_core_chado_generate_vars()
*
* @param $cv_id
* The unique identifier for the cv to retrieve
*
* @return
* An object describing the cv
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cv_by_id($cv_id) {
$r = tripal_core_chado_select('cv', array('*'), array('cv_id' => $cv_id));
return $r;
}
/**
* Retrieve the cv id for the specified CV by name
*
* NOTE: This function is deprecated.
* @see tripal_core_chado_generate_vars()
*
* @param $cv_name
* The unique name for the cv to retrieve
*
* @return
* The numeric cv ID
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cv_id($cv_name) {
$sql = "SELECT cv_id FROM {cv} WHERE name = :name";
$cv = chado_query($sql, array(':name' => $cv_name))->fetchObject();
return $cv->cv_id;
}
/**
* Create an options array to be used in a form element which provides a
* list of all chado cvs
*
* NOTE: This function is deprecated as of Tripal v1.0
*
* @return
* An array(cv_id => name) for each cv in the chado cv table
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cv_options() {
$results = tripal_core_chado_select('cv', array('cv_id', 'name'), array());
$options = array();
foreach ($results as $r) {
$options[$r->cv_id] = $r->name;
}
return $options;
}
/**
* Retrieve a chado cvterm object with a given name
*
* @param $cvterm_id
* the cvterm.cvterm_id
*
* @return
* cvterm array or FALSE on error
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cvterm_by_id($cvterm_id) {
if (!is_numeric($cvterm_id)) {
return FALSE;
}
$values = array('cvterm_id' => $cvterm_id);
$options = array('statement_name' => 'sel_cvterm_id');
$r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
if (!$r) {
return FALSE;
}
return $r[0];
}
/**
* Retrieve a chado cvterm object with a given name
*
* @param $name
* the cvterm.name
* @param $cv_id
* the cv_id of the term you are looking for
* @param $cv_name
* the name of the CV
*
* @return
* cvterm array or FALSE on error
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cvterm_by_name($name, $cv_id = NULL, $cv_name = 'tripal') {
if ($cv_id) {
$values = array(
'name' => $name,
'cv_id' => $cv_id,
);
$options = array(
'statement_name' => 'sel_cvterm_nacv',
'case_insensitive_columns' => array('name')
);
$r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
}
elseif ($cv_name) {
$values = array(
'name' => $name,
'cv_id' => array(
'name' => $cv_name,
),
);
$options = array(
'statement_name' => 'sel_cvterm_nacv',
'case_insensitive_columns' => array('name')
);
$r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
}
else {
$values = array(
'name' => $name,
);
$options = array(
'statement_name' => 'sel_cvterm_na',
'case_insensitive_columns' => array('name')
);
$r = tripal_core_chado_select('cvterm', array('*'), $values, $options);
}
if (!$r) {
return FALSE;
}
if (count($r) > 1) {
watchdog('tripal_cv', "Cannot find a unique term for the term '%name' in the vocabulary '%cv'. Multiple entries exist for this name",
array('%name' => $name, '%cv' => $cv_name ? $cv_name : $cv_id), WATCHDOG_ERROR);
return FALSE;
}
if (count($r) == 0) {
return FALSE;
}
return $r[0];
}
/**
* Retrieve a chado cvterm object with a given name
*
* @param $synonym
* the synonym of the term
* @param $cv_id
* the cv_id of the term you are looking for
* @param $cv_name
* the name of the CV
*
* @return
* cvterm object
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cvterm_by_synonym($synonym, $cv_id = NULL, $cv_name = 'tripal') {
// first find the CVTerm synonym
$values = array(
'synonym' => $synonym,
);
$statement = "sel_cvtermsynonym_sy";
if ($cv_id) {
$values['cvterm_id'] = array('cv_id' => $cv_id);
$statement = "sel_cvtermsynonym_sycv";
}
if ($cv_name) {
$values['cvterm_id'] = array('cv_id' => array('name' => $cv_name));
$statement = "sel_cvtermsynonym_sycv";
}
$options = array(
'statement_name' => $statement,
'case_insensitive_columns' => array('name')
);
$synonym = tripal_core_chado_select('cvtermsynonym', array('cvterm_id'), $values, $options);
// if the synonym doens't exist or more than one record is returned then return false
if (count($synonym) == 0) {
return FALSE;
}
if (count($synonym) > 1) {
return FALSE;
}
// get the cvterm
$values = array('cvterm_id' => $synonym[0]->cvterm_id);
$options = array('statement_name' => 'sel_cvterm_id');
$cvterm = tripal_core_chado_select('cvterm', array('*'), $values, $options);
return $cvterm[0];
}
/**
* Create an options array to be used in a form element
* which provides a list of all chado cvterms
*
* @param $cv_id
* The chado cv_id;
* only cvterms with the supplied cv_id will be returned
* @return
* An array(cvterm_id => name)
* for each cvterm in the chado cvterm table where cv_id=that supplied
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_cvterm_options($cv_id = 0) {
if ($cv_id > 0) {
$results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array('cv_id' => $cv_id));
}
else {
$results = tripal_core_chado_select('cvterm', array('cvterm_id', 'name'), array());
}
$options = array();
foreach ($results as $r) {
$options[$r->cvterm_id] = $r->name;
}
return $options;
}
/**
* Updates the cvtermpath table of Chado for the specified CV.
*
* @param $cv_id
* The chado cv_id;
* @param $job_id
* This function is intended to be used with the Tripal Jobs API.
* When this function is called as a job the $job_id is automatically
* passed to this function.
* @return
* TRUE on success FALSE on failure
*
* @ingroup tripal_cv_api
*/
function tripal_cv_update_cvtermpath($cvid, $job_id = NULL) {
// TODO: need better error checking in this function
// first get the controlled vocabulary name:
$sql = "SELECT * FROM {cv} WHERE cv_id = :cv_id";
$cv = chado_query($sql, array(':cv_id' => $cvid))->fetchObject();
print "\nUpdating cvtermpath for $cv->name...\n";
$previous = tripal_db_set_active('chado');
try {
$sql = "SELECT * FROM fill_cvtermpath(:name)";
db_query($sql, array(':name' => $cv->name));
tripal_db_set_active($previous);
}
catch (Exception $e) {
tripal_db_set_active($previous);
$error = $e->getMessage();
watchdog('tripal_cv', "Could not fill cvtermpath table: @error", array('@error' => $error), WATCHDOG_ERROR);
return FALSE;
}
return TRUE;
}
/**
* Adds a controlled vocabular 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 $comment
* A description or definition of the vocabulary.
*
* @return
* An object populated with fields from the newly added database.
*
* @ingroup tripal_cv_api
*/
function tripal_cv_add_cv($name, $definition) {
// insert/update values
$ins_values = array(
'name' => $name,
'definition' => $definition
);
// see if the CV (default-namespace) exists already in the database
$sel_values = array('name' => $name);
$sel_options = array('statement_name' => 'sel_cv_na');
$results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
// if it does not exists then add it
if (count($results) == 0) {
$ins_options = array('statement_name' => 'ins_cv_nade');
$success = tripal_core_chado_insert('cv', $ins_values, $ins_options);
if (!$success) {
watchdog('tripal_cv', "Failed to create the CV record", NULL, WATCHDOG_WARNING);
return FALSE;
}
$results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
}
// if it already exists then do an update
else {
$upd_options = array('statement_name' => 'upd_cv_nade');
$success = tripal_core_chado_update('cv', $sel_values, $ins_values, $upd_options);
if (!$success) {
watchdog('tripal_cv', "Failed to update the CV record", NULL, WATCHDOG_WARNING);
return FALSE;
}
$results = tripal_core_chado_select('cv', array('*'), $sel_values, $sel_options);
}
// return the cv object
return $results[0];
}
/**
* Add's a CV term to the cvterm table. If the parent CV does not exist then
* that too is added to the CV table. If the cvterm is a relationship term
* then the $is_relationship argument should be set. The function will try
* to first find the relationship in the relationship ontology for updating and
* if it can't be found will add the relationship to the __global CV. 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', 'name' and 'namespace',
* 'is_obsolete', and 'def'. Where 'id' is the term accession, 'name' is the
* term name, 'namespace' is the CV name for the term, 'def' is the term
* definition and 'is_obsolete' is present and set to 1 if the term is defunct.
* The 'id' 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.
* @param $defaultcv
* Optional. 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]
* @param $is_relationship
* If this term is a relationship term then this value should be 1.
* @param $update
* By default this is set to 1. If the term exists it is automatically updated.
* @param $dbname
* In some cases the database name will not be part of the $term['id'] and it
* needs to be explicitly set. Use this argument only if the database name
* cannot be specififed in the term ID (e.g. <DB>:<ACCESSION>).
*
* @return
* A CVTerm object
*
* @ingroup tripal_cv_api
*/
function tripal_cv_add_cvterm($term, $defaultcv = '_global', $is_relationship = 0,
$update = 1, $dbname = 'internal') {
// get the term properties
$id = $term['id'];
$name = '';
$cvname = '';
$definition = '';
$is_obsolete = 0;
$accession = '';
if (array_key_exists('name', $term)) {
$name = $term['name'];
}
else {
$name = $id;
}
if (array_key_exists('namespace', $term)) {
$cvname = $term['namespace'];
}
else {
$cvname = $defaultcv;
}
if (array_key_exists('def', $term)) {
$definition = preg_replace('/^\"(.*)\"/', '\1', $term['def']);
}
else {
$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 !$id) {
watchdog('tripal_cv', "Cannot find cvterm without 'id' or 'name'", NULL, WATCHDOG_WARNING);
return 0;
}
if (!$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) {
watchdog('tripal_cv', "A database name is not provided for this relationship term: $id", NULL, WATCHDOG_WARNING);
return 0;
}
if (!$is_relationship and !$dbname) {
watchdog('tripal_cv', "A database identifier is missing from the term: $id", NULL, WATCHDOG_WARNING);
return 0;
}
// make sure the CV name exists
$cv = tripal_cv_add_cv($cvname, '');
if (!$cv) {
watchdog('tripal_cv', "Cannot find namespace '$cvname' when adding/updating $id", NULL, WATCHDOG_WARNING);
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.
$db = tripal_db_add_db($dbname);
if (!$db) {
watchdog('tripal_cv', "Cannot find database '$dbname' in Chado.", NULL, WATCHDOG_WARNING);
return 0;
}
// the cvterm table has two unique dependencies. We need to check both.
// first check the (name, cv_id, is_obsolete) constraint
$values = array(
'name' => $name,
'is_obsolete' => $is_obsolete,
'cv_id' => array(
'name' => $cvname,
),
);
$options = array('statement_name' => 'sel_cvterm_c1');
$result = tripal_core_chado_select('cvterm', array('*'), $values, $options);
// if the constraint is met then let's check it to see if
// the database name matches the one we have been provided
if (count($result) == 1) {
$cvterm = $result[0];
// get the dbxref record
$values = array('dbxref_id' => $cvterm->dbxref_id);
$options = array('statement_name' => 'sel_dbxref_id');
$result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
$dbxref = $result[0];
// get the db
$values = array('db_id' => $dbxref->db_id);
$options = array('statement_name' => 'sel_db_id');
$result = tripal_core_chado_select('db', array('*'), $values, $options);
$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,
);
$options = array('statement_name' => 'sel_dbxref_idac');
$result = tripal_core_chado_select('dbxref', array('*'), $values, $options);
// if we already have a good dbxref then we want to update our cvterm
// to use this dbxref
if (count($result) > 0) {
$dbxref = $result[0];
$match = array('cvterm_id' => $cvterm->cvterm_id);
$values = array('dbxref_id' => $dbxref->dbxref_id);
$options = array('statement_name' => 'upd_cvterm_db');
$success = tripal_core_chado_update('cvterm', $match, $values, $options);
if (!$success) {
watchdog('tripal_cv', "Failed to correct the dbxref id for the cvterm " .
"'$name' (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
return 0;
}
}
// if we don't have the record 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);
$options = array('statement_name' => 'del_cvterm_cv');
tripal_core_chado_delete('cvterm', $match, $options);
}
}
// check that the accession matches. Sometimes an OBO can define the same term
// multiple times but with different accessions. If this is the case we
// can't do an insert or it will violate the constraint in the cvterm table.
// so we'll need to add the record to the cvterm_dbxref table instead
if ($dbxref->accession != $accession) {
// get/add the dbxref fort his term
$dbxref_new = tripal_db_add_dbxref($db->db_id, $accession);
if (!$dbxref_new) {
watchdog('tripal_cv', "Failed to find or insert the dbxref record for cvterm, " .
"$name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
return 0;
}
// check to see if the cvterm_dbxref record already exists
$values = array(
'cvterm_id' => $cvterm->cvterm_id,
'dbxref_id' => $dbxref_new->dbxref_id,
'is_for_definition' => 1,
);
$options = array('statement_name' => 'sel_cvtermdbxref_cvdbis');
$result = tripal_core_chado_select('cvterm_dbxref', array('*'), $values, $options);
// if the cvterm_dbxref record does not exists then add it
if (count($result)==0) {
$options = array(
'statement_name' => 'ins_cvtermdbxref_cvdbis',
'return_record' => FALSE,
);
$success = tripal_core_chado_insert('cvterm_dbxref', $values, $options);
if (!$success) {
watchdog('tripal_cv', "Failed to find or insert the cvterm_dbxref record for a " .
"duplicated cvterm: $name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
return 0;
}
}
// get the original cvterm with the same name and return that.
$result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':name' => $dbname));
$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, array(':accession' => $accession, ':name' => $dbname));
$cvterm = $result->fetchObject();
if (!$cvterm) {
// check to see if the dbxref exists if not, add it
$dbxref = tripal_db_add_dbxref($db->db_id, $accession);
if (!$dbxref) {
watchdog('tripal_cv', "Failed to find or insert the dbxref record for cvterm, " .
"$name (id: $accession), for database $dbname", NULL, WATCHDOG_WARNING);
return 0;
}
// check to see if the dbxref already has an entry in the cvterm table
// this is the second constraint in the cvterm table
$values = array('dbxref_id' => $dbxref->dbxref_id);
$options = array('statement_name' => 'sel_cvterm_db');
$check = tripal_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
if (count($check) == 0) {
// now add the cvterm
$ins_values = array(
'cv_id' => $cv->cv_id,
'name' => $name,
'definition' => $definition,
'dbxref_id' => $dbxref->dbxref_id,
'is_obsolete' => $is_obsolete,
'is_relationshiptype' => $is_relationship,
);
$ins_options = array('statement_name' => 'ins_cvterm_all');
$success = tripal_core_chado_insert('cvterm', $ins_values, $ins_options);
if (!$success) {
if (!$is_relationship) {
watchdog('tripal_cv', "Failed to insert the term: $name ($dbname)", NULL, WATCHDOG_WARNING);
return 0;
}
else {
watchdog('tripal_cv', "Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)", NULL, WATCHDOG_WARNING);
return 0;
}
}
}
// this dbxref already exists in the cvterm table
else {
watchdog('tripal_cv', "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", NULL, WATCHDOG_WARNING);
return 0;
}
$result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
$cvterm = $result->fetchObject();
}
// upate the cvterm
elseif ($update) {
$match = array('cvterm_id' => $cvterm->cvterm_id);
$upd_values = array(
'name' => $name,
'definition' => $definition,
'is_obsolete' => $is_obsolete,
'is_relationshiptype' => $is_relationship,
);
$upd_options = array('statement_name' => 'upd_cvterm_nadeisis');
$success = tripal_core_chado_update('cvterm', $match, $upd_values, $upd_options);
if (!$success) {
watchdog('tripal_cv', "Failed to update the term: $name", NULL, WATCHDOG_WARNING);
return 0;
}
$result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
$cvterm = $result->fetchObject();
}
else {
// do nothing, we have the cvterm but we don't want to update
}
// return the cvterm
return $cvterm;
}
/**
* This function defines the custom tables that will be created
* in the chado schema.
*
* @ingroup tripal_cv_api
*/
function tripal_cv_get_custom_tables($table = NULL) {
if (!$table or strcmp($table, 'tripal_obo_temp')==0) {
$schema['tripal_obo_temp'] = array(
'table' => 'tripal_obo_temp',
'fields' => array(
'id' => array(
'type' => 'varchar',
'length' => '255',
'not null' => TRUE,
),
'stanza' => array(
'type' => 'text',
'not null' => TRUE,
),
'type' => array(
'type' => 'varchar',
'length' => '50',
'not null' => TRUE,
),
),
'indexes' => array(
'tripal_obo_temp_idx0' => array('id'),
'tripal_obo_temp_idx0' => array('type'),
),
'unique keys' => array(
'tripal_obo_temp_uq0' => array('id'),
),
);
}
return $schema;
}
/**
* This function allows other modules to programatically
* submit an ontology for loading into Chado. This function
* will add a job to the Jobs subsystem for parsing the ontology.
* You can either pass a known OBO ID to the function or the URL
* or full path the the ontology file. If a URL or file name is
* passed then the $obo_name argument must also be provided. If
* this is the first time the ontology has been provided to Tripal
* then it will be added to the database and will be assigned a
* unique OBO ID.
*
* @param $obo_id
* If the ontology is already loaded into the Tripal tables then
* use this argument to specify the unique ID for the ontology
* that will be loaded
* @param $obo_name
* If the OBO has not been added before then use this argument
* to specify the human readable name of the ontology.
* @param $obo_url
* If the OBO to be loaded is located on a remote server then
* use this argument to provide the URL.
* @param $obo_file
* If the OBO is housed on the local file system of the server then
* use this argument to specify the full path.
*
* @return
* returns the job_id of the submitted job or FALSE if the job was not added
*
* @ingroup tripal_cv_api
*/
function tripal_cv_submit_obo_job($obo_id = NULL, $obo_name = NULL, $obo_url = NULL, $obo_file = NULL) {
global $user;
if ($obo_id) {
$sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = :obo_id";
$obo = db_query($sql, array(':obo_id' => $obo_id))->fetchObject();
$args = array($obo_id);
return tripal_add_job("Load OBO $obo->name", 'tripal_cv',
"tripal_cv_load_obo_v1_2_id", $args, $user->uid);
}
else {
if ($obo_url) {
$args = array($obo_name, $obo_url);
return tripal_add_job("Load OBO $obo_name", 'tripal_cv',
"tripal_cv_load_obo_v1_2_url", $args, $user->uid);
}
elseif ($obo_file) {
$args = array($obo_name, $obo_file);
return tripal_add_job("Load OBO $obo_name", 'tripal_cv',
"tripal_cv_load_obo_v1_2_file", $args, $user->uid);
}
}
return FALSE;
}
/**
* Add the obo to the tripal_cv_obo table in the Drupal database
*
* @param $name
* The human readable name of this ontology
* @param $path
* The file path or URL of the ontology
*
* @return
* Returns the ontology ID
*
* @ingroup tripal_cv_api
*/
function tripal_cv_add_obo_ref($name, $path) {
$record = new stdClass;
$record->name = $name;
$record->path = $path;
drupal_write_record('tripal_cv_obo', $record);
return $record->obo_id;
}
/**
* 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 $string
* The string to search for
*
* @return
* A json array of terms that begin with the provided string
*
* @ingroup tripal_cv_api
*/
function tripal_cv_cvterm_name_autocomplete($cv_id, $string = '') {
$sql = "
SELECT cvterm_id, name
FROM {cvterm}
WHERE cv_id = :cv_id and name like :name
ORDER by name
LIMIT 25 OFFSET 0
";
$results = chado_query($sql, array(':cv_id' => $cv_id, ':name' => $string . '%'));
$items = array();
foreach ($results as $term) {
$items[$term->name] = $term->name;
}
drupal_json_output($items);
}