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@@ -1,866 +1,917 @@
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<?php
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-/**
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+/**
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+ * @file
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+ * Tripal Ontology Loader
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+ *
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* @defgroup tripal_obo_loader Tripal Ontology Loader
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* @ingroup tripal_cv
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*/
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-
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_load_obo_v1_2_id($obo_id,$jobid = NULL){
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-
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- // get the OBO reference
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- $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
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- $obo = db_fetch_object(db_query($sql,$obo_id));
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-
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- // if the reference is for a remote URL then run the URL processing function
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- if(preg_match("/^http:\/\//",$obo->path) or preg_match("/^ftp:\/\//",$obo->path)){
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- tripal_cv_load_obo_v1_2_url($obo->name,$obo->path,$jobid,0);
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- }
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- // if the reference is for a local file then run the file processing function
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- else {
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- // check to see if the file is located local to Drupal
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- $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $obo->path;
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- if(file_exists($dfile)){
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- tripal_cv_load_obo_v1_2_file($obo->name,$dfile,$jobid,0);
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- }
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- // if not local to Drupal, the file must be someplace else, just use
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- // the full path provided
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- else{
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- if(file_exists($obo->path)){
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- tripal_cv_load_obo_v1_2_file($obo->name,$obo->path,$jobid,0);
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- } else {
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- print "ERROR: counld not find OBO file: '$obo->path'\n";
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- }
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_load_obo_v1_2_id($obo_id, $jobid = NULL) {
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+
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+ // get the OBO reference
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+ $sql = "SELECT * FROM {tripal_cv_obo} WHERE obo_id = %d";
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+ $obo = db_fetch_object(db_query($sql, $obo_id));
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+
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+ // if the reference is for a remote URL then run the URL processing function
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+ if (preg_match("/^http:\/\//", $obo->path) or preg_match("/^ftp:\/\//", $obo->path)) {
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+ tripal_cv_load_obo_v1_2_url($obo->name, $obo->path, $jobid, 0);
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+ }
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+ // if the reference is for a local file then run the file processing function
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+ else {
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+ // check to see if the file is located local to Drupal
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+ $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $obo->path;
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+ if (file_exists($dfile)) {
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+ tripal_cv_load_obo_v1_2_file($obo->name, $dfile , $jobid, 0);
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+ }
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+ // if not local to Drupal, the file must be someplace else, just use
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+ // the full path provided
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+ else {
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+ if (file_exists($obo->path)) {
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+ tripal_cv_load_obo_v1_2_file($obo->name, $obo->path, $jobid, 0);
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}
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- }
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+ else {
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+ print "ERROR: counld not find OBO file: '$obo->path'\n";
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+ }
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+ }
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+ }
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}
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_load_obo_v1_2_file($obo_name,$file,$jobid = NULL,$is_new = 1){
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- $newcvs = array();
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-
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- tripal_cv_load_obo_v1_2($file,$jobid,$newcvs);
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- if($is_new){
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- tripal_cv_load_obo_add_ref($obo_name,$file);
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- }
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- // update the cvtermpath table
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- tripal_cv_load_update_cvtermpath($newcvs,$jobid);
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- print "Ontology Sucessfully loaded!\n";
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_load_obo_v1_2_file($obo_name, $file, $jobid = NULL, $is_new = TRUE) {
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+ $newcvs = array();
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+
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+ tripal_cv_load_obo_v1_2($file, $jobid, $newcvs);
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+ if ($is_new) {
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+ tripal_cv_load_obo_add_ref($obo_name, $file);
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+ }
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+
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+ // update the cvtermpath table
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+ tripal_cv_load_update_cvtermpath($newcvs, $jobid);
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+ print "Ontology Sucessfully loaded!\n";
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+
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}
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_load_obo_v1_2_url($obo_name,$url,$jobid = NULL,$is_new = 1){
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-
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- $newcvs = array();
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-
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- // first download the OBO
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- $temp = tempnam(sys_get_temp_dir(),'obo_');
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- print "Downloading URL $url, saving to $temp\n";
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- $url_fh = fopen($url,"r");
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- $obo_fh = fopen($temp,"w");
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- if(!$url_fh){
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- tripal_cv_obo_quiterror("Unable to download the remote OBO file at $url. Could a firewall be blocking outgoing connections? ".
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- " if you are unable to download the file you may manually downlod the OBO file and use the web interface to ".
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- " specify the location of the file on your server.");
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-
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- }
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- while(!feof($url_fh)){
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- fwrite($obo_fh,fread($url_fh,255),255);
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- }
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- fclose($url_fh);
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- fclose($obo_fh);
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-
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- // second, parse the OBO
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- tripal_cv_load_obo_v1_2($temp,$jobid,$newcvs);
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-
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- // now remove the temp file
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- unlink($temp);
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-
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- if($is_new){
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- tripal_cv_load_obo_add_ref($obo_name,$url);
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- }
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-
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- // update the cvtermpath table
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- tripal_cv_load_update_cvtermpath($newcvs,$jobid);
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-
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- print "Ontology Sucessfully loaded!\n";
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_load_obo_v1_2_url($obo_name, $url, $jobid = NULL, $is_new = TRUE) {
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+
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+ $newcvs = array();
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+
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+ // first download the OBO
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+ $temp = tempnam(sys_get_temp_dir(), 'obo_');
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+ print "Downloading URL $url, saving to $temp\n";
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+ $url_fh = fopen($url, "r");
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+ $obo_fh = fopen($temp, "w");
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+ if (!$url_fh) {
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+ tripal_cv_obo_quiterror("Unable to download the remote OBO file at $url. Could a firewall be blocking outgoing connections? ".
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+ " if you are unable to download the file you may manually downlod the OBO file and use the web interface to ".
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+ " specify the location of the file on your server.");
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+
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+ }
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+ while (!feof($url_fh)) {
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+ fwrite($obo_fh, fread($url_fh, 255), 255);
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+ }
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+ fclose($url_fh);
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+ fclose($obo_fh);
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+
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+ // second, parse the OBO
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+ tripal_cv_load_obo_v1_2($temp, $jobid, $newcvs);
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+
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+ // now remove the temp file
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+ unlink($temp);
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+
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+ if ($is_new) {
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+ tripal_cv_load_obo_add_ref($obo_name, $url);
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+ }
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+
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+ // update the cvtermpath table
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+ tripal_cv_load_update_cvtermpath($newcvs, $jobid);
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+
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+ print "Ontology Sucessfully loaded!\n";
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}
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_load_update_cvtermpath($newcvs,$jobid){
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-
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- print "\nUpdating cvtermpath table. This may take a while...\n";
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- foreach($newcvs as $namespace => $cvid){
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- tripal_cv_update_cvtermpath($cvid, $jobid);
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- }
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_load_update_cvtermpath($newcvs, $jobid) {
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+
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+ print "\nUpdating cvtermpath table. This may take a while...\n";
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+ foreach ($newcvs as $namespace => $cvid) {
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+ tripal_cv_update_cvtermpath($cvid, $jobid);
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+ }
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}
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+
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/**
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-*
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-*/
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-function tripal_cv_load_obo_add_ref($name,$path){
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- $isql = "INSERT INTO tripal_cv_obo (name,path) VALUES ('%s','%s')";
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- db_query($isql,$name,$path);
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+ *
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+ */
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+function tripal_cv_load_obo_add_ref($name, $path) {
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+ $isql = "INSERT INTO {tripal_cv_obo} (name,path) VALUES ('%s','%s')";
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+ db_query($isql, $name, $path);
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}
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_load_obo_v1_2($file,$jobid = NULL,&$newcvs) {
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-
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- global $previous_db;
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-
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- $header = array();
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- $obo = array();
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-
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- print "Opening File $file\n";
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-
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- // set the search path
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- $previous_db = tripal_db_set_active('chado');
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-
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- // make sure we have an 'internal' and a '_global' database
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- if(!tripal_cv_obo_add_db('internal')){
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- tripal_cv_obo_quiterror("Cannot add 'internal' database");
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- }
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- if(!tripal_cv_obo_add_db('_global')){
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- tripal_cv_obo_quiterror("Cannot add '_global' database");
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- }
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-
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- // parse the obo file
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- tripal_cv_obo_parse($file,$obo,$header);
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-
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- // add the CV for this ontology to the database
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- $defaultcv = tripal_cv_obo_add_cv($header['default-namespace'][0],'');
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- if(!$defaultcv){
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- tripal_cv_obo_quiterror('Cannot add namespace ' . $header['default-namespace'][0]);
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- }
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- $newcvs[$header['default-namespace'][0]] = $defaultcv->cv_id;
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-
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- // add any typedefs to the vocabulary first
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- $typedefs = $obo['Typedef'];
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- foreach($typedefs as $typedef){
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- tripal_cv_obo_process_term($typedef,$defaultcv,$obo,1,$newcvs);
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- }
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-
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- // next add terms to the vocabulary
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- $terms = $obo['Term'];
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- if(!tripal_cv_obo_process_terms($terms,$defaultcv,$obo,$jobid,$newcvs)){
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- tripal_cv_obo_quiterror('Cannot add terms from this ontology');
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- }
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- return tripal_cv_obo_loader_done();
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
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+ global $_tripal_cv_previous_db;
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+
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+ $header = array();
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+ $obo = array();
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+
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+ print "Opening File $file\n";
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+
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+ // set the search path
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+ $_tripal_cv_previous_db = tripal_db_set_active('chado');
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+
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+ // make sure we have an 'internal' and a '_global' database
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+ if (!tripal_cv_obo_add_db('internal')) {
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+ tripal_cv_obo_quiterror("Cannot add 'internal' database");
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+ }
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+ if (!tripal_cv_obo_add_db('_global')) {
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+ tripal_cv_obo_quiterror("Cannot add '_global' database");
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+ }
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+
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+ // parse the obo file
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+ tripal_cv_obo_parse($file, $obo, $header);
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+
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+ // add the CV for this ontology to the database
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+ $defaultcv = tripal_cv_obo_add_cv($header['default-namespace'][0], '');
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+ if (!$defaultcv) {
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+ tripal_cv_obo_quiterror('Cannot add namespace ' . $header['default-namespace'][0]);
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+ }
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+ $newcvs[$header['default-namespace'][0]] = $defaultcv->cv_id;
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+
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+ // add any typedefs to the vocabulary first
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+ $typedefs = $obo['Typedef'];
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+ foreach ($typedefs as $typedef) {
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+ tripal_cv_obo_process_term($typedef, $defaultcv, $obo, 1, $newcvs);
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+ }
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+
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+ // next add terms to the vocabulary
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+ $terms = $obo['Term'];
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+ if (!tripal_cv_obo_process_terms($terms, $defaultcv, $obo, $jobid, $newcvs)) {
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+ tripal_cv_obo_quiterror('Cannot add terms from this ontology');
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+ }
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+
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+ return tripal_cv_obo_loader_done();
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}
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_obo_quiterror ($message){
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- print "ERROR: $message\n";
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- db_query("set search_path to public");
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- exit;
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_obo_quiterror($message) {
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+
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+ print "ERROR: $message\n";
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+ db_query("set search_path to public");
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+ exit;
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+
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}
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_obo_loader_done (){
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- // return the search path to normal
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- tripal_db_set_active($previous_db);
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- db_query("set search_path to public");
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- return '';
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_obo_loader_done() {
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+
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+ // return the search path to normal
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+ tripal_db_set_active($_tripal_cv_previous_db);
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+ db_query("set search_path to public");
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+
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+ return '';
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}
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+
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/**
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-*
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-* @ingroup tripal_obo_loader
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-*/
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-function tripal_cv_obo_process_terms($terms,$defaultcv,$obo,$jobid=null,&$newcvs){
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-
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- $i = 0;
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- $count = sizeof($terms);
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- $interval = intval($count * 0.01);
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- if($interval > 1){
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- $interval = 1;
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- }
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-
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- foreach ($terms as $term){
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-
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- // update the job status every 1% terms
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- if($jobid and $i % $interval == 0){
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- tripal_job_set_progress($jobid,intval(($i/$count)*50)); // we mulitply by 50 because parsing and loacing cvterms
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- // is only the first half. The other half is updating
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- } // the cvtermpath table.
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-
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- if(!tripal_cv_obo_process_term($term,$defaultcv,$obo,0,$newcvs)){
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- tripal_cv_obo_quiterror("Failed to process terms from the ontology");
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- }
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- $i++;
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- }
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- return 1;
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+ *
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+ * @ingroup tripal_obo_loader
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+ */
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+function tripal_cv_obo_process_terms($terms, $defaultcv, $obo, $jobid = NULL, &$newcvs) {
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+
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+ $i = 0;
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+ $count = sizeof($terms);
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+ $interval = intval($count * 0.01);
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+ if ($interval > 1) {
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+ $interval = 1;
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+ }
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+
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+ foreach ($terms as $term) {
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+
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+ // update the job status every 1% terms
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+ if ($jobid and $i % $interval == 0) {
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+ tripal_job_set_progress($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,$cvterm)){
|
|
|
- tripal_cv_obo_quiterror("Cannot add synonyms");
|
|
|
+ *
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_process_term($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 $alt_id");
|
|
|
}
|
|
|
- }
|
|
|
- // reformat the deprecated 'exact_synonym, narrow_synonym, and broad_synonym'
|
|
|
- // types to be of the v1.2 standard
|
|
|
- if(isset($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['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['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,$cvterm)){
|
|
|
- tripal_cv_obo_quiterror("Cannot add/update synonyms");
|
|
|
+ }
|
|
|
+ if (isset($term['broad_synonym'])) {
|
|
|
+ foreach ($term['broad_synonym'] as $synonym) {
|
|
|
+ $new = preg_replace('/^\s*(\".+?\")(.*?)$/', '$1 BROAD $2', $synonym);
|
|
|
+ $term['synonym'][] = $new;
|
|
|
}
|
|
|
- }
|
|
|
- // add the comment to the cvtermprop table
|
|
|
- if(isset($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");
|
|
|
- }
|
|
|
- $j++;
|
|
|
+ }
|
|
|
+
|
|
|
+ if (!tripal_cv_obo_add_synonyms($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, $j)) {
|
|
|
+ tripal_cv_obo_quiterror("Cannot add/update cvterm property");
|
|
|
}
|
|
|
- }
|
|
|
- // add any other external dbxrefs
|
|
|
- if(isset($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).");
|
|
|
- }
|
|
|
+ $j++;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ // add any other external dbxrefs
|
|
|
+ if (isset($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_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,$xref)){
|
|
|
- tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
|
|
|
- }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (isset($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: $is_a");
|
|
|
- }
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // add is_a relationships for this cvterm
|
|
|
+ if (isset($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['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($term['builtin'])){
|
|
|
- //print "WARNING: unhandled tag: builtin\n";
|
|
|
- }
|
|
|
- return 1;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (isset($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($term['builtin'])) {
|
|
|
+ //print "WARNING: unhandled tag: builtin\n";
|
|
|
+ }
|
|
|
+ return 1;
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_add_db($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 $db;
|
|
|
+ * Add a database record
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_add_db($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 $db;
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_add_cv($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 $cv;
|
|
|
+ * Add a controlled vocab record
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_add_cv($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 $cv;
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_add_relationship($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 1;
|
|
|
+ * 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 $term;
|
|
|
- }
|
|
|
+ *
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_get_term($obo, $id) {
|
|
|
+ foreach ($obo as $type) {
|
|
|
+ foreach ($type as $term) {
|
|
|
+ $accession = $term['id'][0];
|
|
|
+ if (strcmp($accession, $id)==0) {
|
|
|
+ return $term;
|
|
|
}
|
|
|
- }
|
|
|
- return;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return FALSE;
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_add_synonyms($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");
|
|
|
+ *
|
|
|
+ * @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");
|
|
|
+ }
|
|
|
}
|
|
|
- $syncv = db_fetch_object(db_query($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);
|
|
|
- $type = strtolower(preg_replace('/^.*"\s+(.*?)\s+.*$/','\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 1;
|
|
|
+
|
|
|
+ // 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,$dbxref);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ */
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return TRUE;
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_parse($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
|
|
|
- $stanza = array();
|
|
|
- continue;
|
|
|
+ * Actually parse the OBO file
|
|
|
+ *
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_parse($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]], $stanza);
|
|
|
+ }
|
|
|
}
|
|
|
- // break apart the line into the tag and value but ignore any escaped colons
|
|
|
- preg_replace("/\\:/","|-|-|",$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();
|
|
|
+ // 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();
|
|
|
}
|
|
|
- if(!isset($obo[$type][$stanza['id'][0]])){
|
|
|
- $obo[$type][$stanza['id'][0]] = $stanza;
|
|
|
- } else {
|
|
|
- array_merge($obo[$type][$stanza['id'][0]],$stanza);
|
|
|
+ $header[$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]], $stanza);
|
|
|
+ }
|
|
|
+ }
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_add_cvterm_dbxref($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 0;
|
|
|
- }
|
|
|
-
|
|
|
- // 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: $xref");
|
|
|
- }
|
|
|
- }
|
|
|
- return 1;
|
|
|
+ * Add database reference to cvterm
|
|
|
+ *
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_add_cvterm_dbxref($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: $xref");
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ return TRUE;
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_add_cvterm_prop($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 $property for term\n");
|
|
|
- }
|
|
|
- return 1;
|
|
|
+ * Add property to CVterm
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_add_cvterm_prop($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 $dbname");
|
|
|
+ *
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_add_cvterm($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;
|
|
|
}
|
|
|
-
|
|
|
- // 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";
|
|
|
- }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ 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: $dbname)");
|
|
|
+ }
|
|
|
}
|
|
|
- elseif($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";
|
|
|
- }
|
|
|
+ if (!$is_relationship) {
|
|
|
+ print "Added CV term: $name ($dbname)\n";
|
|
|
}
|
|
|
- elseif($check and strcmp($check->name,$name)==0){
|
|
|
- // this entry already exists. We're good, so do nothing
|
|
|
+ else {
|
|
|
+ print "Added relationship CV term: $name ($dbname)\n";
|
|
|
}
|
|
|
- $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname));
|
|
|
- }
|
|
|
- elseif($update) { // update the cvterm
|
|
|
+ }
|
|
|
+ elseif ($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
|
|
|
$sql = "
|
|
|
- UPDATE {cvterm} SET name='%s', definition='%s',
|
|
|
- is_obsolete = %d, is_relationshiptype = %d
|
|
|
- WHERE cvterm_id = %d
|
|
|
+ UPDATE {cvterm} SET name = '%s', definition = '%s',
|
|
|
+ is_obsolete = %d, is_relationshiptype = %d
|
|
|
+ WHERE dbxref_id = %d
|
|
|
";
|
|
|
- if(!db_query($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";
|
|
|
+ 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";
|
|
|
}
|
|
|
- }
|
|
|
- // return the cvterm
|
|
|
- return $cvterm;
|
|
|
+ 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 $cvterm;
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
-*
|
|
|
-* @ingroup tripal_obo_loader
|
|
|
-*/
|
|
|
-function tripal_cv_obo_add_dbxref($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 $dbxref;
|
|
|
+ * Add Database Reference
|
|
|
+ * @ingroup tripal_obo_loader
|
|
|
+ */
|
|
|
+function tripal_cv_obo_add_dbxref($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;
|
|
|
|
|
|
}
|
|
|
|
Lacey Sanderson