<?php
/**
* @file
* Tripal Ontology Loader
*
* @defgroup tripal_obo_loader Tripal Ontology Loader
* @ingroup tripal_cv
*/
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_load_obo_v1_2_id($obo_id, $jobid = NULL) {
// get the OBO reference
$sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
$obo = db_fetch_object(db_query($sql, $obo_id));
// if the reference is for a remote URL then run the URL processing function
if (preg_match("/^http:\/\//", $obo->path) or preg_match("/^ftp:\/\//", $obo->path)) {
tripal_cv_load_obo_v1_2_url($obo->name, $obo->path, $jobid, 0);
}
// if the reference is for a local file then run the file processing function
else {
// check to see if the file is located local to Drupal
$dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $obo->path;
if (file_exists($dfile)) {
tripal_cv_load_obo_v1_2_file($obo->name, $dfile , $jobid, 0);
}
// if not local to Drupal, the file must be someplace else, just use
// the full path provided
else {
if (file_exists($obo->path)) {
tripal_cv_load_obo_v1_2_file($obo->name, $obo->path, $jobid, 0);
}
else {
print "ERROR: counld not find OBO file: '$obo->path'\n";
}
}
}
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_load_obo_v1_2_file($obo_name, $file, $jobid = NULL, $is_new = TRUE) {
$newcvs = array();
tripal_cv_load_obo_v1_2($file, $jobid, $newcvs);
if ($is_new) {
tripal_cv_load_obo_add_ref($obo_name, $file);
}
// update the cvtermpath table
tripal_cv_load_update_cvtermpath($newcvs, $jobid);
print "Ontology Sucessfully loaded!\n";
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_load_obo_v1_2_url($obo_name, $url, $jobid = NULL, $is_new = TRUE) {
$newcvs = array();
// first download the OBO
$temp = tempnam(sys_get_temp_dir(), 'obo_');
print "Downloading URL $url, saving to $temp\n";
$url_fh = fopen($url, "r");
$obo_fh = fopen($temp, "w");
if (!$url_fh) {
tripal_cv_obo_quiterror("Unable to download the remote OBO file at $url. Could a firewall be blocking outgoing connections? ".
" if you are unable to download the file you may manually downlod the OBO file and use the web interface to ".
" specify the location of the file on your server.");
}
while (!feof($url_fh)) {
fwrite($obo_fh, fread($url_fh, 255), 255);
}
fclose($url_fh);
fclose($obo_fh);
// second, parse the OBO
tripal_cv_load_obo_v1_2($temp, $jobid, $newcvs);
// now remove the temp file
unlink($temp);
if ($is_new) {
tripal_cv_load_obo_add_ref($obo_name, $url);
}
// update the cvtermpath table
tripal_cv_load_update_cvtermpath($newcvs, $jobid);
print "Ontology Sucessfully loaded!\n";
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_load_update_cvtermpath($newcvs, $jobid) {
print "\nUpdating cvtermpath table. This may take a while...\n";
foreach ($newcvs as $namespace => $cvid) {
tripal_cv_update_cvtermpath($cvid, $jobid);
}
}
/**
*
*/
function tripal_cv_load_obo_add_ref($name, $path) {
$isql = "INSERT INTO {tripal_cv_obo} (name,path) VALUES ('%s','%s')";
db_query($isql, $name, $path);
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
global $_tripal_cv_previous_db;
$header = array();
$obo = array();
print "Opening File $file\n";
// set the search path
$_tripal_cv_previous_db = tripal_db_set_active('chado');
// make sure we have an 'internal' and a '_global' database
if (!tripal_cv_obo_add_db('internal')) {
tripal_cv_obo_quiterror("Cannot add 'internal' database");
}
if (!tripal_cv_obo_add_db('_global')) {
tripal_cv_obo_quiterror("Cannot add '_global' database");
}
// parse the obo file
tripal_cv_obo_parse($file, $obo, $header);
// add the CV for this ontology to the database
$defaultcv = tripal_cv_obo_add_cv($header['default-namespace'][0], '');
if (!$defaultcv) {
tripal_cv_obo_quiterror('Cannot add namespace ' . $header['default-namespace'][0]);
}
$newcvs[$header['default-namespace'][0]] = $defaultcv->cv_id;
// add any typedefs to the vocabulary first
$typedefs = $obo['Typedef'];
foreach ($typedefs as $typedef) {
tripal_cv_obo_process_term($typedef, $defaultcv, $obo, 1, $newcvs);
}
// next add terms to the vocabulary
$terms = $obo['Term'];
if (!tripal_cv_obo_process_terms($terms, $defaultcv, $obo, $jobid, $newcvs)) {
tripal_cv_obo_quiterror('Cannot add terms from this ontology');
}
return tripal_cv_obo_loader_done();
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_quiterror($message) {
print "ERROR: $message\n";
db_query("set search_path to public");
exit;
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_loader_done() {
// return the search path to normal
tripal_db_set_active($_tripal_cv_previous_db);
db_query("set search_path to public");
return '';
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_process_terms($terms, $defaultcv, $obo, $jobid = NULL, &$newcvs) {
$i = 0;
$count = sizeof($terms);
$interval = intval($count * 0.01);
if ($interval > 1) {
$interval = 1;
}
foreach ($terms as $term) {
// update the job status every 1% terms
if ($jobid and $i % $interval == 0) {
tripal_job_set_progress($jobid, intval(($i / $count) * 50)); // we mulitply by 50 because parsing and loacing cvterms
// is only the first half. The other half is updating
} // the cvtermpath table.
if (!tripal_cv_obo_process_term($term, $defaultcv, $obo, 0, $newcvs)) {
tripal_cv_obo_quiterror("Failed to process terms from the ontology");
}
$i++;
}
return 1;
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_process_term($term, $defaultcv, $obo, $is_relationship = 0, &$newcvs) {
// add the cvterm
$cvterm = tripal_cv_obo_add_cvterm($term, $defaultcv, $is_relationship, 1);
if (!$cvterm) {
tripal_cv_obo_quiterror("Cannot add the term " . $term['id'][0]);
}
if ($term['namespace'][0]) {
$newcvs[$term['namespace'][0]] = $cvterm->cv_id;
}
// now handle other properites
if (isset($term['is_anonymous'])) {
//print "WARNING: unhandled tag: is_anonymous\n";
}
if (isset($term['alt_id'])) {
foreach ($term['alt_id'] as $alt_id) {
if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $alt_id)) {
tripal_cv_obo_quiterror("Cannot add alternate id $alt_id");
}
}
}
if (isset($term['subset'])) {
//print "WARNING: unhandled tag: subset\n";
}
// add synonyms for this cvterm
if (isset($term['synonym'])) {
if (!tripal_cv_obo_add_synonyms($term, $cvterm)) {
tripal_cv_obo_quiterror("Cannot add synonyms");
}
}
// reformat the deprecated 'exact_synonym, narrow_synonym, and broad_synonym'
// types to be of the v1.2 standard
if (isset($term['exact_synonym']) or isset($term['narrow_synonym']) or isset($term['broad_synonym'])) {
if (isset($term['exact_synonym'])) {
foreach ($term['exact_synonym'] as $synonym) {
$new = preg_replace('/^\s*(\".+?\")(.*?)$/', '$1 EXACT $2', $synonym);
$term['synonym'][] = $new;
}
}
if (isset($term['narrow_synonym'])) {
foreach ($term['narrow_synonym'] as $synonym) {
$new = preg_replace('/^\s*(\".+?\")(.*?)$/', '$1 NARROW $2', $synonym);
$term['synonym'][] = $new;
}
}
if (isset($term['broad_synonym'])) {
foreach ($term['broad_synonym'] as $synonym) {
$new = preg_replace('/^\s*(\".+?\")(.*?)$/', '$1 BROAD $2', $synonym);
$term['synonym'][] = $new;
}
}
if (!tripal_cv_obo_add_synonyms($term, $cvterm)) {
tripal_cv_obo_quiterror("Cannot add/update synonyms");
}
}
// add the comment to the cvtermprop table
if (isset($term['comment'])) {
$comments = $term['comment'];
$j = 0;
foreach ($comments as $comment) {
if (!tripal_cv_obo_add_cvterm_prop($cvterm, 'comment', $comment, $j)) {
tripal_cv_obo_quiterror("Cannot add/update cvterm property");
}
$j++;
}
}
// add any other external dbxrefs
if (isset($term['xref'])) {
foreach ($term['xref'] as $xref) {
if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref)) {
tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
}
}
}
if (isset($term['xref_analog'])) {
foreach ($term['xref_analog'] as $xref) {
if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref)) {
tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
}
}
}
if (isset($term['xref_unk'])) {
foreach ($term['xref_unk'] as $xref) {
if (!tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref)) {
tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
}
}
}
// add is_a relationships for this cvterm
if (isset($term['is_a'])) {
foreach ($term['is_a'] as $is_a) {
if (!tripal_cv_obo_add_relationship($cvterm, $defaultcv, $obo, 'is_a', $is_a, $is_relationship)) {
tripal_cv_obo_quiterror("Cannot add relationship is_a: $is_a");
}
}
}
if (isset($term['intersection_of'])) {
//print "WARNING: unhandled tag: intersection_of\n";
}
if (isset($term['union_of'])) {
//print "WARNING: unhandled tag: union_on\n";
}
if (isset($term['disjoint_from'])) {
//print "WARNING: unhandled tag: disjoint_from\n";
}
if (isset($term['relationship'])) {
foreach ($term['relationship'] as $value) {
$rel = preg_replace('/^(.+?)\s.+?$/', '\1', $value);
$object = preg_replace('/^.+?\s(.+?)$/', '\1', $value);
if (!tripal_cv_obo_add_relationship($cvterm, $defaultcv, $obo, $rel, $object, $is_relationship)) {
tripal_cv_obo_quiterror("Cannot add relationship $rel: $object");
}
}
}
if (isset($term['replaced_by'])) {
//print "WARNING: unhandled tag: replaced_by\n";
}
if (isset($term['consider'])) {
//print "WARNING: unhandled tag: consider\n";
}
if (isset($term['use_term'])) {
//print "WARNING: unhandled tag: user_term\n";
}
if (isset($term['builtin'])) {
//print "WARNING: unhandled tag: builtin\n";
}
return 1;
}
/**
* Add a database record
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_db($dbname) {
$db_sql = "SELECT * FROM {db} WHERE name ='%s'";
$db = db_fetch_object(db_query($db_sql, $dbname));
if (!$db) {
if (!db_query("INSERT INTO {db} (name) VALUES ('%s')", $dbname)) {
tripal_cv_obo_quiterror("Cannot create '$dbname' db in Chado.");
}
$db = db_fetch_object(db_query($db_sql, $dbname));
}
return $db;
}
/**
* Add a controlled vocab record
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_cv($name, $comment) {
// see if the CV (default-namespace) exists already in the database
$vocab = $name;
$remark = $comment;
$cv_sql = "SELECT * FROM {cv} WHERE name = '%s'";
$cv = db_fetch_object(db_query($cv_sql, $vocab));
// if the CV exists then update it, otherwise insert
if (!$cv) {
$sql = "INSERT INTO {cv} (name,definition) VALUES ('%s','%s')";
if (!db_query($sql, $vocab, $remark)) {
tripal_cv_obo_quiterror("Failed to create the CV record");
}
$cv = db_fetch_object(db_query($cv_sql, $vocab));
}
else {
$sql = "UPDATE {cv} SET definition = '%s' WHERE name ='%s'";
if (!db_query($sql, $remark, $vocab)) {
tripal_cv_obo_quiterror("Failed to update the CV record");
}
$cv = db_fetch_object(db_query($cv_sql, $vocab));
}
return $cv;
}
/**
* Add a cvterm relationship
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_relationship($cvterm, $defaultcv, $obo, $rel, $objname, $object_is_relationship = 0) {
// make sure the relationship cvterm exists
$term = array(
'name' => array($rel),
'id' => array($rel),
'definition' => array(''),
'is_obsolete' => array(0),
);
$relcvterm = tripal_cv_obo_add_cvterm($term, $defaultcv, 1, 0);
if (!$relcvterm) {
tripal_cv_obo_quiterror("Cannot find or insert the relationship term: $rel\n");
}
// get the object term
$objterm = tripal_cv_obo_get_term($obo, $objname);
if (!$objterm) {
tripal_cv_obo_quiterror("Could not find object term $objname\n");
}
$objcvterm = tripal_cv_obo_add_cvterm($objterm, $defaultcv, $object_is_relationship, 1);
if (!$objcvterm) {
tripal_cv_obo_quiterror("Cannot add/find cvterm");
}
// check to see if the cvterm_relationship already exists, if not add it
$cvrsql = "SELECT * FROM {cvterm_relationship} WHERE type_id = %d and subject_id = %d and object_id = %d";
if (!db_fetch_object(db_query($cvrsql, $relcvterm->cvterm_id, $cvterm->cvterm_id, $objcvterm->cvterm_id))) {
$sql = "INSERT INTO {cvterm_relationship} ".
"(type_id,subject_id,object_id) VALUES (%d,%d,%d)";
if (!db_query($sql, $relcvterm->cvterm_id, $cvterm->cvterm_id, $objcvterm->cvterm_id)) {
tripal_cv_obo_quiterror("Cannot add term relationship: '$cvterm->name' $rel '$objcvterm->name'");
}
}
return TRUE;
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_get_term($obo, $id) {
foreach ($obo as $type) {
foreach ($type as $term) {
$accession = $term['id'][0];
if (strcmp($accession, $id)==0) {
return $term;
}
}
}
return FALSE;
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_synonyms($term, $cvterm) {
// make sure we have a 'synonym_type' vocabulary
$sql = "SELECT * FROM {cv} WHERE name='synonym_type'";
$syncv = db_fetch_object(db_query($sql));
if (!$syncv) {
$sql = "INSERT INTO {cv} (name,definition) VALUES ('synonym_type','')";
if (!db_query($sql)) {
tripal_cv_obo_quiterror("Failed to add the synonyms type vocabulary");
}
$syncv = db_fetch_object(db_query($sql));
}
// now add the synonyms
if (isset($term['synonym'])) {
foreach ($term['synonym'] as $synonym) {
// separate out the synonym definition and the synonym type
$def = preg_replace('/^\s*"(.*)"\s*.*$/', '\1', $synonym);
$type = drupal_strtolower(preg_replace('/^.*"\s+(.*?)\s+.*$/', '\1', $synonym));
// make sure the synonym type exists in the 'synonym_type' vocabulary
$cvtsql = "
SELECT *
FROM {cvterm} CVT
INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
WHERE CVT.name = '%s' and CV.name = '%s'
";
$syntype = db_fetch_object(db_query($cvtsql, $type, 'synonym_type'));
if (!$syntype) {
// build a 'term' object so we can add the missing term
$term = array(
'name' => array($type),
'id' => array("internal:$type"),
'definition' => array(''),
'is_obsolete' => array(0),
);
$syntype = tripal_cv_obo_add_cvterm($term, $syncv, 0, 1);
if (!$syntype) {
tripal_cv_obo_quiterror("Cannot add synonym type: internal:$type");
}
}
// make sure the synonym doesn't already exists
$sql = "
SELECT *
FROM {cvtermsynonym}
WHERE cvterm_id = %d and synonym = '%s'
";
$syn = db_fetch_object(db_query($sql, $cvterm->cvterm_id, $def));
if (!$syn) {
$sql = "INSERT INTO {cvtermsynonym} (cvterm_id,synonym,type_id)
VALUES(%d,'%s',%d)";
if (!db_query($sql, $cvterm->cvterm_id, $def, $syntype->cvterm_id)) {
tripal_cv_obo_quiterror("Failed to insert the synonym for term: $name ($def)");
}
}
// now add the dbxrefs for the synonym if we have a comma in the middle
// of a description then this will cause problems when splitting os lets
// just change it so it won't mess up our splitting and then set it back
// later.
/**
$synonym = preg_replace('/(".*?),\s(.*?")/','$1,_$2',$synonym);
$dbxrefs = preg_split("/, /",preg_replace('/^.*\[(.*?)\]$/','\1',$synonym));
foreach ($dbxrefs as $dbxref) {
$dbxref = preg_replace('/,_/',", ",$dbxref);
if ($dbxref) {
tripal_cv_obo_add_cvterm_dbxref($syn,$dbxref);
}
}
*/
}
}
return TRUE;
}
/**
* Actually parse the OBO file
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_parse($obo_file, &$obo, &$header) {
$i = 0;
$in_header = 1;
$stanza = array();
// iterate through the lines in the OBO file and parse the stanzas
$fh = fopen($obo_file, 'r');
while ($line = fgets($fh)) {
$i++;
// remove newlines
$line = rtrim($line);
// remove any special characters that may be hiding
$line = preg_replace('/[^(\x20-\x7F)]*/', '', $line);
// skip empty lines
if (strcmp($line, '') == 0) {
continue;
}
//remove comments from end of lines
$line = preg_replace('/^(.*?)\!.*$/', '\1', $line); // TODO: if the explamation is escaped
if (preg_match('/^\s*\[/', $line)) { // at the first stanza we're out of header
$in_header = 0;
// load the stanza we just finished reading
if (sizeof($stanza) > 0) {
if (!isset($obo[$type])) {
$obo[$type] = array();
}
if (!isset($obo[$type][$stanza['id'][0]])) {
$obo[$type][$stanza['id'][0]] = $stanza;
}
else {
array_merge($obo[$type][$stanza['id'][0]], $stanza);
}
}
// get the stanza type: Term, Typedef or Instance
$type = preg_replace('/^\s*\[\s*(.+?)\s*\]\s*$/', '\1', $line);
// start fresh with a new array
$stanza = array();
continue;
}
// break apart the line into the tag and value but ignore any escaped colons
preg_replace("/\\:/", "|-|-|", $line); // temporarily replace escaped colons
$pair = explode(":", $line, 2);
$tag = $pair[0];
$value = ltrim(rtrim($pair[1]));// remove surrounding spaces
$tag = preg_replace("/\|-\|-\|/", "\:", $tag); // return the escaped colon
$value = preg_replace("/\|-\|-\|/", "\:", $value);
if ($in_header) {
if (!isset($header[$tag])) {
$header[$tag] = array();
}
$header[$tag][] = $value;
}
else {
if (!isset($stanza[$tag])) {
$stanza[$tag] = array();
}
$stanza[$tag][] = $value;
}
}
// now add the last term in the file
if (sizeof($stanza) > 0) {
if (!isset($obo[$type])) {
$obo[$type] = array();
}
if (!isset($obo[$type][$stanza['id'][0]])) {
$obo[$type][$stanza['id'][0]] = $stanza;
}
else {
array_merge($obo[$type][$stanza['id'][0]], $stanza);
}
}
}
/**
* Add database reference to cvterm
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref) {
$dbname = preg_replace('/^(.+?):.*$/', '$1', $xref);
$accession = preg_replace('/^.+?:\s*(.*?)(\{.+$|\[.+$|\s.+$|\".+$|$)/', '$1', $xref);
$description = preg_replace('/^.+?\"(.+?)\".*?$/', '$1', $xref);
$dbxrefs = preg_replace('/^.+?\[(.+?)\].*?$/', '$1', $xref);
if (!$accession) {
tripal_cv_obo_quiterror();
watchdog('tripal_cv', "Cannot add a dbxref without an accession: '$xref'", NULL, WATCHDOG_WARNING);
return FALSE;
}
// if the xref is a database link, handle that specially
if (strcmp($dbname, 'http') == 0) {
$accession = $xref;
$dbname = 'URL';
}
// check to see if the database exists
$db = tripal_cv_obo_add_db($dbname);
if (!$db) {
tripal_cv_obo_quiterror("Cannot find database '$dbname' in Chado.");
}
// now add the dbxref
$dbxref = tripal_cv_obo_add_dbxref($db->db_id, $accession, '', $description);
if (!$dbxref) {
tripal_cv_obo_quiterror("Cannot find or add the database reference (dbxref)");
}
// finally add the cvterm_dbxref but first check to make sure it exists
$sql = "SELECT * from {cvterm_dbxref} WHERE cvterm_id = %d and dbxref_id = %d";
if (!db_fetch_object(db_query($sql, $cvterm->cvterm_id, $dbxref->dbxref_id))) {
$sql = "INSERT INTO {cvterm_dbxref} (cvterm_id,dbxref_id)".
"VALUES (%d,%d)";
if (!db_query($sql, $cvterm->cvterm_id, $dbxref->dbxref_id)) {
tripal_cv_obo_quiterror("Cannot add cvterm_dbxref: $xref");
}
}
return TRUE;
}
/**
* Add property to CVterm
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_cvterm_prop($cvterm, $property, $value, $rank) {
// make sure the 'cvterm_property_type' CV exists
$cv = tripal_cv_obo_add_cv('cvterm_property_type', '');
if (!$cv) {
tripal_cv_obo_quiterror("Cannot add/find cvterm_property_type cvterm");
}
// get the property type cvterm. If it doesn't exist then we want to add it
$sql = "
SELECT *
FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
WHERE CVT.name = '%s' and CV.name = '%s'
";
$cvproptype = db_fetch_object(db_query($sql, $property, 'cvterm_property_type'));
if (!$cvproptype) {
$term = array(
'name' => array($property),
'id' => array("internal:$property"),
'definition' => array(''),
'is_obsolete' => array(0),
);
$cvproptype = tripal_cv_obo_add_cvterm($term, $cv, 0, 0);
if (!$cvproptype) {
tripal_cv_obo_quiterror("Cannot add cvterm property: internal:$property");
}
}
// remove any properties that currently exist for this term. We'll reset them
if ($rank == 0) {
$sql = "DELETE FROM {cvtermprop} WHERE cvterm_id = %d";
db_query($sql, $cvterm->cvterm_id);
}
// now add the property
$sql = "INSERT INTO {cvtermprop} (cvterm_id,type_id,value,rank) ".
"VALUES (%d, %d, '%s',%d)";
if (!db_query($sql, $cvterm->cvterm_id, $cvproptype->cvterm_id, $value, $rank)) {
tripal_cv_obo_quiterror("Could not add property $property for term\n");
}
return TRUE;
}
/**
*
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_cvterm($term, $defaultcv, $is_relationship = 0, $update = 1) {
// get the term properties
$id = $term['id'][0];
$name = $term['name'][0];
$cvname = $term['namespace'][0];
$definition = preg_replace('/^\"(.*)\"/', '\1', $term['def'][0]);
$is_obsolete = 0;
if (isset($term['is_obsolete'][0]) and strcmp($term['is_obsolete'][0], 'true') == 0) {
$is_obsolete = 1;
}
if (!$cvname) {
$cvname = $defaultcv->name;
}
// make sure the CV name exists
$cv = tripal_cv_obo_add_cv($cvname, '');
if (!$cv) {
tripal_cv_obo_quiterror("Cannot find namespace '$cvname' when adding/updating $id");
}
// this SQL statement will be used a lot to find a cvterm so just set it
// here for easy reference below.
$cvtermsql = "SELECT CVT.name, CVT.cvterm_id, DB.name as dbname, DB.db_id
FROM {cvterm} CVT
INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
INNER JOIN {db} DB on DBX.db_id = DB.db_id
INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
WHERE CVT.name = '%s' and DB.name = '%s'";
// get the accession and the database from the cvterm
if (preg_match('/^.+?:.*$/', $id)) {
$accession = preg_replace('/^.+?:(.*)$/', '\1', $id);
$dbname = preg_replace('/^(.+?):.*$/', '\1', $id);
}
if ($is_relationship and !$dbname) {
$accession = $id;
// because this is a relationship cvterm first check to see if it
// exists in the relationship ontology. If it does then return the cvterm.
// If not then set the dbname to _global and we'll add it or find it there
$cvterm = db_fetch_object(db_query($cvtermsql, $name, 'OBO_REL'));
if ($cvterm) {
return $cvterm;
}
else {
// next check if this term is in the _global ontology. If it is then
// return it no matter what the original CV
$dbname = '_global';
$cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
if ($cvterm) {
return $cvterm;
}
}
}
if (!$is_relationship and !$dbname) {
tripal_cv_obo_quiterror("A database identifier is missing from the term: $id");
}
// check to see if the database exists.
$db = tripal_cv_obo_add_db($dbname);
if (!$db) {
tripal_cv_obo_quiterror("Cannot find database '$dbname' in Chado.");
}
// if the cvterm doesn't exist then add it otherwise just update it
$cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
if (!$cvterm) {
// check to see if the dbxref exists if not, add it
$dbxref = tripal_cv_obo_add_dbxref($db->db_id, $accession);
if (!$dbxref) {
tripal_cv_obo_quiterror("Failed to find or insert the dbxref record for cvterm, $name (id: $accession), for database $dbname");
}
// check to see if the dbxref already has an entry in the cvterm table
$sql = "SELECT * FROM {cvterm} WHERE dbxref_id = %d";
$check = db_fetch_object(db_query($sql, $dbxref->dbxref_id));
if (!$check) {
// now add the cvterm
$sql = "
INSERT INTO {cvterm} (cv_id, name, definition, dbxref_id,
is_obsolete, is_relationshiptype)
VALUES (%d,'%s','%s',%d,%d,%d)
";
if (!db_query($sql, $cv->cv_id, $name, $definition,
$dbxref->dbxref_id, $is_obsolete, $is_relationship)) {
if (!$is_relationship) {
tripal_cv_obo_quiterror("Failed to insert the term: $name ($dbname)");
}
else {
tripal_cv_obo_quiterror("Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)");
}
}
if (!$is_relationship) {
print "Added CV term: $name ($dbname)\n";
}
else {
print "Added relationship CV term: $name ($dbname)\n";
}
}
elseif ($check and strcmp($check->name, $name)!=0) {
// this dbxref_id alrady exists in the database but the name is
// different. We will trust that the OBO is correct and that there
// has been a name change for this dbxref, so we'll update
$sql = "
UPDATE {cvterm} SET name = '%s', definition = '%s',
is_obsolete = %d, is_relationshiptype = %d
WHERE dbxref_id = %d
";
if (!db_query($sql, $name, $definition, $is_obsolete, $is_relationship, $dbxref->dbxref_id)) {
if (!$is_relationship) {
tripal_cv_obo_quiterror("Failed to update the term: $name ($dbname)");
}
else {
tripal_cv_obo_quiterror("Failed to update the relationship term: $name (cv: " . $cvname . " db: $dbname)");
}
}
if (!$is_relationship) {
print "Updated CV term: $name ($dbname)\n";
}
else {
print "Updated relationship CV term: $name ($dbname)\n";
}
}
elseif ($check and strcmp($check->name, $name)==0) {
// this entry already exists. We're good, so do nothing
}
$cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
}
elseif ($update) { // update the cvterm
$sql = "
UPDATE {cvterm} SET name='%s', definition='%s',
is_obsolete = %d, is_relationshiptype = %d
WHERE cvterm_id = %d
";
if (!db_query($sql, $term['name'][0], $definition,
$is_obsolete, $is_relationship, $cvterm->cvterm_id)) {
tripal_cv_obo_quiterror("Failed to update the term: $name");
}
$cvterm = db_fetch_object(db_query($cvtermsql, $name, $dbname));
if (!$is_relationship) {
print "Updated CV term: $name ($dbname)\n";
}
else {
print "Updated relationship CV term: $name ($dbname)\n";
}
}
// return the cvterm
return $cvterm;
}
/**
* Add Database Reference
* @ingroup tripal_obo_loader
*/
function tripal_cv_obo_add_dbxref($db_id, $accession, $version='', $description='') {
// check to see if the dbxref exists if not, add it
$dbxsql = "SELECT dbxref_id FROM {dbxref} WHERE db_id = %d and accession = '%s'";
$dbxref = db_fetch_object(db_query($dbxsql, $db_id, $accession));
if (!$dbxref) {
$sql = "
INSERT INTO {dbxref} (db_id, accession, version, description)
VALUES (%d,'%s','%s','%s')
";
if (!db_query($sql, $db_id, $accession, $version, $description)) {
tripal_cv_obo_quiterror("Failed to insert the dbxref record $accession");
}
print "Added Dbxref accession: $accession\n";
$dbxref = db_fetch_object(db_query($dbxsql, $db_id, $accession));
}
return $dbxref;
}