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@@ -1,10 +1,100 @@
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<?php
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+/*************************************************************************
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+*
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+*/
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+function tripal_cv_load_obo_v1_2_id($obo_id,$jobid = NULL){
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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,$jobid,0);
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+ }
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+ // if not local to Drupal, the file must be someplace else, just use
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+ // the full path provided
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+ else{
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+ tripal_cv_load_obo_v1_2_file($obo->name,$obo->path,$jobid,0);
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+ }
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+ }
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+}
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/*************************************************************************
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*
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*/
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-function tripal_cv_load_obo_v1_2($file) {
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+function tripal_cv_load_obo_v1_2_file($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,$jobid);
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+ print "Ontology Sucessfully loaded!\n";
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+}
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+/*************************************************************************
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+*
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+*/
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+function tripal_cv_load_obo_v1_2_url($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(tripal_get_moddir('tripal_cv'),'obo_');
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+ print "Opening URL $url\n";
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+ $url_fh = fopen($url,"r");
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+ $obo_fh = fopen($temp,"w");
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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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+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, $jobid);
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+ }
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+}
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+/*************************************************************************
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+*
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+*/
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+function tripal_cv_load_obo_add_ref($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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+function tripal_cv_load_obo_v1_2($file,$jobid = NULL,&$newcvs) {
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$header = array();
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$obo = array();
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@@ -16,137 +106,195 @@ function tripal_cv_load_obo_v1_2($file) {
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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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- return tripal_cv_obo_loader_done();
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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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- return tripal_cv_obo_loader_done();
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+ tripal_cv_obo_quiterror("Cannot add '_global' database");
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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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// add the CV for this ontology to the database
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- $cv = tripal_cv_obo_add_cv($header['default-namespace'][0],'');
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- if(!$cv){
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- return tripal_cv_obo_loader_done();
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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]] = $defaultcv->cv_id;
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// add any typedefs to the vocabulary first
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$typedefs = $obo['Typedef'];
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foreach($typedefs as $typedef){
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- tripal_cv_obo_process_stanza($typedef,$cv,1);
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+ tripal_cv_obo_process_term($typedef,$defaultcv,$obo,1,$newcvs);
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}
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// next add terms to the vocabulary
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$terms = $obo['Term'];
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- if(!tripal_cv_obo_process_stanza($terms,$cv,$obo)){
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- return tripal_cv_obo_loader_done();
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+ if(!tripal_cv_obo_process_terms($terms,$defaultcv,$obo,$jobid,$newcvs)){
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+ tripal_cv_obo_quiterror('Cannot add terms from this ontology');
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}
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return tripal_cv_obo_loader_done();
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}
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-
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/*************************************************************************
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*
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*/
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-function tripal_cv_obo_process_stanza($terms,$cv,$obo,$is_relationship=0){
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+function tripal_cv_obo_quiterror ($message){
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+ print "ERROR: $message\n";
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+ db_query("set search_path to public");
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+ exit;
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+}
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+/*************************************************************************
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+*
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+*/
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+function tripal_cv_obo_loader_done (){
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+ // return the search path to normal
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+ db_query("set search_path to public");
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+ return '';
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+}
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+/*************************************************************************
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+*
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+*/
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+function tripal_cv_obo_process_terms($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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foreach ($terms as $term){
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- // add the cvterm
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- $cvterm = tripal_cv_obo_add_cv_term($term,$cv,$is_relationship,1);
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- if(!$cvterm){ return 0; }
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+ // update the job status every 1% terms
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+ if($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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- // now handle other properites
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- if(isset($term['is_anonymous'])){
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- print "WARNING: unhandled tag: is_anonymous\n";
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+ if(!tripal_cv_obo_process_term($term,$defaultcv,$obo,0,$newcvs)){
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+ tripal_cv_obo_quiterror("Failed to process terms from the ontology");
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}
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- if(isset($term['alt_id'])){
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- foreach($term['alt_id'] as $alt_id){
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- if(!tripal_cv_obo_add_cvterm_dbxref($cvterm,$alt_id)){
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- return 0;
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- }
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+ $i++;
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+ }
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+ return 1;
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+}
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+/*************************************************************************
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+*
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+*/
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+
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+function tripal_cv_obo_process_term($term,$defaultcv,$obo,$is_relationship=0,&$newcvs){
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+
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+ // add the cvterm
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+ $cvterm = tripal_cv_obo_add_cv_term($term,$defaultcv,$is_relationship,1);
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+ if(!$cvterm){
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+ tripal_cv_obo_quiterror("Cannot add the term " . $term['id'][0]);
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+ }
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+ if($term['namespace'][0]){
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+ $newcvs[$term['namespace'][0]] = $cvterm->cv_id;
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+ }
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+
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+ // now handle other properites
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+ if(isset($term['is_anonymous'])){
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+ print "WARNING: unhandled tag: is_anonymous\n";
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+ }
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+ if(isset($term['alt_id'])){
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+ foreach($term['alt_id'] as $alt_id){
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+ if(!tripal_cv_obo_add_cvterm_dbxref($cvterm,$alt_id)){
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+ tripal_cv_obo_quiterror("Cannot add alternate id $alt_id");
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}
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}
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- if(isset($term['subset'])){
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- print "WARNING: unhandled tag: subset\n";
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- }
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- // add synonyms for this cvterm
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- if(isset($term['synonym'])){
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- if(!tripal_cv_obo_add_synonyms($term,$cvterm)){
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- return 0;
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- }
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+ }
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+ if(isset($term['subset'])){
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+ print "WARNING: unhandled tag: subset\n";
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+ }
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+ // add synonyms for this cvterm
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+ if(isset($term['synonym'])){
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+ if(!tripal_cv_obo_add_synonyms($term,$cvterm)){
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+ tripal_cv_obo_quiterror("Cannot add synonyms");
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}
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+ }
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+ // reformat the deprecated 'exact_synonym, narrow_synonym, and broad_synonym'
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+ // types to be of the v1.2 standard
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+ if(isset($term['exact_synonym']) or isset($term['narrow_synonym']) or isset($term['broad_synonym'])){
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if(isset($term['exact_synonym'])){
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- // depricated
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- print "WARNING: unhandled tag: exact_synonym\n";
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+ foreach ($term['exact_synonym'] as $synonym){
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+
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+ $new = preg_replace('/^\s*(\".+?\")(.*?)$/','$1 EXACT $2',$synonym);
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+ $term['synonym'][] = $new;
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+ }
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}
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if(isset($term['narrow_synonym'])){
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- print "WARNING: unhandled tag: narrow_synonym\n";
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- // depricated
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+ foreach ($term['narrow_synonym'] as $synonym){
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+ $new = preg_replace('/^\s*(\".+?\")(.*?)$/','$1 NARROW $2',$synonym);
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+ $term['synonym'][] = $new;
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+ }
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}
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if(isset($term['broad_synonym'])){
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- print "WARNING: unhandled tag: broad_synonym\n";
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- // depricated
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+ foreach ($term['broad_synonym'] as $synonym){
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+ $new = preg_replace('/^\s*(\".+?\")(.*?)$/','$1 BROAD $2',$synonym);
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+ $term['synonym'][] = $new;
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+ }
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+ }
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+
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+ if(!tripal_cv_obo_add_synonyms($term,$cvterm)){
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+ tripal_cv_obo_quiterror("Cannot add/update synonyms");
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}
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- // add the comment to the cvtermprop table
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- if(isset($term['comment'])){
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- $comments = $term['comment'];
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- $j = 0;
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- foreach($comments as $comment){
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- if(!tripal_cv_obo_add_cvterm_prop($cvterm,'comment',$comment,$j)){
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- return 0;
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- }
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- $j++;
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+ }
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+ // add the comment to the cvtermprop table
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+ if(isset($term['comment'])){
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+ $comments = $term['comment'];
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+ $j = 0;
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+ foreach($comments as $comment){
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+ if(!tripal_cv_obo_add_cvterm_prop($cvterm,'comment',$comment,$j)){
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+ tripal_cv_obo_quiterror("Cannot add/update cvterm property");
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}
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- }
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- // add any other external dbxrefs
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- if(isset($term['xref']) or isset($term['xref_analog']) or isset($term['xref_unk'])){
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- foreach($term['xref'] as $xref){
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- if(!tripal_cv_obo_add_cvterm_dbxref($cvterm,$xref)){
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- return 0;
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- }
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+ $j++;
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+ }
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+ }
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+ // add any other external dbxrefs
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+ if(isset($term['xref']) or isset($term['xref_analog']) or isset($term['xref_unk'])){
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+ foreach($term['xref'] as $xref){
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+ if(!tripal_cv_obo_add_cvterm_dbxref($cvterm,$xref)){
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+ tripal_cv_obo_quiterror("Cannot add/update cvterm database reference (dbxref).");
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}
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}
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+ }
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- // add is_a relationships for this cvterm
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- if(isset($term['is_a'])){
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- foreach($term['is_a'] as $is_a){
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- if(!tripal_cv_obo_add_relationship($cvterm,$cv,$obo,'is_a',$is_a)){
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- return 0;
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- }
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+ // add is_a relationships for this cvterm
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+ if(isset($term['is_a'])){
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+ foreach($term['is_a'] as $is_a){
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+ if(!tripal_cv_obo_add_relationship($cvterm,$defaultcv,$obo,'is_a',$is_a,$is_relationship)){
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+ tripal_cv_obo_quiterror("Cannot add relationship is_a: $is_a");
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}
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- }
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- if(isset($term['intersection_of'])){
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- print "WARNING: unhandled tag: intersection_of\n";
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}
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- if(isset($term['union_of'])){
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- print "WARNING: unhandled tag: union_on\n";
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- }
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- if(isset($term['disjoint_from'])){
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- print "WARNING: unhandled tag: disjoint_from\n";
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- }
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- if(isset($term['relationship'])){
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- foreach($term['relationship'] as $value){
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- $rel = preg_replace('/^(.+?)\s.+?$/','\1',$value);
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- $object = preg_replace('/^.+?\s(.+?)$/','\1',$value);
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- if(!tripal_cv_obo_add_relationship($cvterm,$cv,$obo,$rel,$object)){
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- return 0;
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- }
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+ }
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+ if(isset($term['intersection_of'])){
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+ print "WARNING: unhandled tag: intersection_of\n";
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+ }
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+ if(isset($term['union_of'])){
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+ print "WARNING: unhandled tag: union_on\n";
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+ }
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+ if(isset($term['disjoint_from'])){
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+ print "WARNING: unhandled tag: disjoint_from\n";
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+ }
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+ if(isset($term['relationship'])){
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+ foreach($term['relationship'] as $value){
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+ $rel = preg_replace('/^(.+?)\s.+?$/','\1',$value);
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+ $object = preg_replace('/^.+?\s(.+?)$/','\1',$value);
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+ if(!tripal_cv_obo_add_relationship($cvterm,$defaultcv,$obo,$rel,$object,$is_relationship)){
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+ tripal_cv_obo_quiterror("Cannot add relationship $rel: $object");
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}
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}
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- if(isset($term['replaced_by'])){
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- print "WARNING: unhandled tag: replaced_by\n";
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- }
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- if(isset($term['consider'])){
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- print "WARNING: unhandled tag: consider\n";
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- }
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- if(isset($term['use_term'])){
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- print "WARNING: unhandled tag: user_term\n";
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- }
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- if(isset($term['builtin'])){
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- print "WARNING: unhandled tag: builtin\n";
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- }
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- }
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+ }
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+ if(isset($term['replaced_by'])){
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+ print "WARNING: unhandled tag: replaced_by\n";
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+ }
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+ if(isset($term['consider'])){
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+ print "WARNING: unhandled tag: consider\n";
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+ }
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+ if(isset($term['use_term'])){
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+ print "WARNING: unhandled tag: user_term\n";
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+ }
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+ if(isset($term['builtin'])){
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+ print "WARNING: unhandled tag: builtin\n";
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+ }
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return 1;
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}
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/*************************************************************************
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@@ -158,8 +306,7 @@ function tripal_cv_obo_add_db($dbname){
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$db = db_fetch_object(db_query($db_sql,$dbname));
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if(!$db){
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if(!db_query("INSERT INTO {db} (name) VALUES ('%s')",$dbname)){
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- print "Cannot create '$dbname' db in Chado.";
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- return 0;
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+ tripal_cv_obo_quiterror("Cannot create '$dbname' db in Chado.");
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}
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$db = db_fetch_object(db_query($db_sql,$dbname));
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}
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@@ -180,15 +327,13 @@ function tripal_cv_obo_add_cv($name,$comment){
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if(!$cv){
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$sql = "INSERT INTO {cv} (name,definition) VALUES ('%s','%s')";
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if(!db_query($sql,$vocab,$remark)){
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- print "Failed to create the CV record";
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- return 0;
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+ tripal_cv_obo_quiterror("Failed to create the CV record");
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}
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$cv = db_fetch_object(db_query($cv_sql,$vocab));
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} else {
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$sql = "UPDATE {cv} SET definition = '%s' WHERE name ='%s'";
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if(!db_query($sql,$remark,$vocab)){
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- print "Failed to update the CV record";
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- return 0;
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+ tripal_cv_obo_quiterror("Failed to update the CV record");
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}
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$cv = db_fetch_object(db_query($cv_sql,$vocab));
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}
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@@ -201,7 +346,9 @@ function tripal_cv_obo_add_cvterm_prop($cvterm,$property,$value,$rank){
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// make sure the 'cvterm_property_type' CV exists
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$cv = tripal_cv_obo_add_cv($property,'');
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- if(!$cv){ return 0; }
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+ if(!$cv){
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+ tripal_cv_obo_quiterror("Cannot add/find cvterm_property_type cvterm");
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+ }
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// get the property type cvterm. If it doesn't exist then we want to add it
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$sql = "
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@@ -218,7 +365,9 @@ function tripal_cv_obo_add_cvterm_prop($cvterm,$property,$value,$rank){
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'is_obsolete' => array(0),
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);
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$cvproptype = tripal_cv_obo_add_cv_term($term,$cv,0,0);
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- if(!$cvproptype){ return 0; }
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+ if(!$cvproptype){
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+ tripal_cv_obo_quiterror("Cannot add/upste cvterm property: internal:$property");
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+ }
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}
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@@ -232,56 +381,45 @@ function tripal_cv_obo_add_cvterm_prop($cvterm,$property,$value,$rank){
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$sql = "INSERT INTO {cvtermprop} (cvterm_id,type_id,value,rank) ".
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"VALUES (%d, %d, '%s',%d)";
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if(!db_query($sql,$cvterm->cvterm_id,$cvproptype->cvterm_id,$value,$rank)){
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- print "Could not add property $property for term\n";
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- return 0;
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+ tripal_cv_obo_quiterror("Could not add property $property for term\n");
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}
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return 1;
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}
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/*************************************************************************
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*
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*/
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-function tripal_cv_obo_add_relationship($cvterm,$cv,$obo,$rel,$objname){
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+function tripal_cv_obo_add_relationship($cvterm,$defaultcv,$obo,$rel,$objname,$object_is_relationship=0){
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// make sure the relationship cvterm exists
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- $sql = "
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- SELECT *
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- FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
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- WHERE CVT.name = '%s' and CV.name = '%s'
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- ";
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- $cvisa = db_fetch_object(db_query($sql,$rel,$cv->name));
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- if(!$cvisa){
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- $term = array(
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- 'name' => array($rel),
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- 'id' => array($rel),
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- 'definition' => array(''),
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- 'is_obsolete' => array(0),
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- );
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- if(!tripal_cv_obo_add_cv_term($term,$cv,1,1)){
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- print "Cannot find or insert the relationship term: $rel.\n";
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- return 0;
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- }
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- $cvisa = db_fetch_object(db_query($sql,$rel,$cv->name));
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+ $term = array(
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+ 'name' => array($rel),
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+ 'id' => array($rel),
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+ 'definition' => array(''),
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+ 'is_obsolete' => array(0),
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+ );
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+ $relcvterm = tripal_cv_obo_add_cv_term($term,$defaultcv,1,0);
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+ if(!$relcvterm){
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+ tripal_cv_obo_quiterror("Cannot find or insert the relationship term: $rel\n");
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}
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// get the object term
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$objterm = tripal_cv_obo_get_term($obo,$objname);
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if(!$objterm) {
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- print "Could not find object term $objname\n";
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- return 0;
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+ tripal_cv_obo_quiterror("Could not find object term $objname\n");
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+ }
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+ $objcvterm = tripal_cv_obo_add_cv_term($objterm,$defaultcv,$object_is_relationship,1);
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+ if(!$objcvterm){
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+ tripal_cv_obo_quiterror("Cannot add/find cvterm");
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}
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- $objcvterm = tripal_cv_obo_add_cv_term($objterm,$cv,1,1);
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- if(!$objcvterm){ return 0; }
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// check to see if the cvterm_relationship already exists, if not add it
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$cvrsql = "SELECT * FROM {cvterm_relationship} WHERE type_id = %d and subject_id = %d and object_id = %d";
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- if(!db_fetch_object(db_query($cvrsql,$cvisa->cvterm_id,$cvterm->cvterm_id,$objcvterm->cvterm_id))){
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+ if(!db_fetch_object(db_query($cvrsql,$relcvterm->cvterm_id,$cvterm->cvterm_id,$objcvterm->cvterm_id))){
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$sql = "INSERT INTO {cvterm_relationship} ".
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"(type_id,subject_id,object_id) VALUES (%d,%d,%d)";
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- if(!db_query($sql,$cvisa->cvterm_id,$cvterm->cvterm_id,$objcvterm->cvterm_id)){
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- print "Cannot add $rel relationship";
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- return 0;
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+ if(!db_query($sql,$relcvterm->cvterm_id,$cvterm->cvterm_id,$objcvterm->cvterm_id)){
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+ tripal_cv_obo_quiterror("Cannot add term relationship: '$cvterm->name' $rel '$objcvterm->name'");
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}
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-// print " $rel $objname\n";
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}
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return 1;
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@@ -311,8 +449,7 @@ function tripal_cv_obo_add_synonyms($term,$cvterm){
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if(!$syncv){
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$sql = "INSERT INTO {cv} (name,definition) VALUES ('synonym_type','')";
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if(!db_query($sql)){
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- print "Failed to add the synonyms type vocabulary";
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- return 0;
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+ tripal_cv_obo_quiterror("Failed to add the synonyms type vocabulary");
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}
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}
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@@ -340,7 +477,7 @@ function tripal_cv_obo_add_synonyms($term,$cvterm){
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'is_obsolete' => array(0),
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);
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if(!tripal_cv_obo_add_cv_term($term,$syncv,0,1)){
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- return 0;
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+ tripal_cv_obo_quiterror("Cannot add synonym type: internal:$type");
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}
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$syntype = db_fetch_object(db_query($cvtsql,$type,'synonym_type'));
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}
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@@ -356,10 +493,22 @@ function tripal_cv_obo_add_synonyms($term,$cvterm){
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$sql = "INSERT INTO {cvtermsynonym} (cvterm_id,synonym,type_id)
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VALUES(%d,'%s',%d)";
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if(!db_query($sql,$cvterm->cvterm_id,$def,$syntype->cvterm_id)){
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- print "Failed to insert the synonym for term: $name ($def)\n";
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- return 0;
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+ tripal_cv_obo_quiterror("Failed to insert the synonym for term: $name ($def)");
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}
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- }
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+ }
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+
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+ // now add the dbxrefs for the synonym if we have a comma in the middle
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+ // of a description then this will cause problems when splitting os lets
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+ // just change it so it won't mess up our splitting and then set it back
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+ // later.
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+// $synonym = preg_replace('/(".*?),\s(.*?")/','$1,_$2',$synonym);
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+// $dbxrefs = preg_split("/, /",preg_replace('/^.*\[(.*?)\]$/','\1',$synonym));
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+// foreach($dbxrefs as $dbxref){
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+// $dbxref = preg_replace('/,_/',", ",$dbxref);
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+// if($dbxref){
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+// tripal_cv_obo_add_cvterm_dbxref($syn,$dbxref);
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+// }
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+// }
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}
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}
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return 1;
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@@ -367,45 +516,77 @@ function tripal_cv_obo_add_synonyms($term,$cvterm){
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/*************************************************************************
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*
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*/
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-function tripal_cv_obo_add_cv_term($term,$cv,$is_relationship = 0,$update = 1){
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+function tripal_cv_obo_add_cv_term($term,$defaultcv,$is_relationship = 0,$update = 1){
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// get the term properties
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$id = $term['id'][0];
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$name = $term['name'][0];
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+ $cvname = $term['namespace'][0];
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$definition = preg_replace('/^\"(.*)\"/','\1',$term['def'][0]);
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$is_obsolete = 0;
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if(isset($term['is_obsolete'][0]) and strcmp($term['is_obsolete'][0],'true')==0){
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$is_obsolete = 1;
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}
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+ if(!$cvname){
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+ $cvname = $defaultcv->name;
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+ }
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+ // make sure the CV name exists
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+ $cv = tripal_cv_obo_add_cv($cvname,'');
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+ if(!$cv){
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+ tripal_cv_obo_quiterror("Cannot find namespace '$cvname' when adding/updating $id");
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+ }
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+
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+ // this SQL statement will be used a lot to find a cvterm so just set it
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+ // here for easy reference below.
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+ $cvtermsql = "SELECT CVT.name, CVT.cvterm_id, DB.name as dbname, DB.db_id
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+ FROM {cvterm} CVT
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+ INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
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+ INNER JOIN {db} DB on DBX.db_id = DB.db_id
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+ INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
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+ WHERE CVT.name = '%s' and DB.name = '%s'";
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// get the accession and the database from the cvterm
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if(preg_match('/^.+?:.*$/',$id)){
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$accession = preg_replace('/^.+?:(.*)$/','\1',$id);
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$dbname = preg_replace('/^(.+?):.*$/','\1',$id);
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}
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- else if($is_relationship) {
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+ if($is_relationship and !$dbname){
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$accession = $id;
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- $dbname = 'OBO_REL';
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+ // because this is a relationship cvterm first check to see if it
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+ // exists in the relationship ontology. If it does then return the cvterm.
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+ // If not then set the dbname to _global and we'll add it or find it there
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+ $cvterm = db_fetch_object(db_query($cvtermsql,$name,'OBO_REL'));
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+ if($cvterm){
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+ return $cvterm;
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+ } else {
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+ // next check if this term is in the _global ontology. If it is then
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+ // return it no matter what the original CV
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+ $dbname = '_global';
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+
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+ $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname));
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+ if($cvterm){
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+ return $cvterm;
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+ }
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+ }
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+ }
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+ if(!$is_relationship and !$dbname){
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+ tripal_cv_obo_quiterror("A database identifier is missing from the term: $id");
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}
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- // check to see if the database exists
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+ // check to see if the database exists.
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$db = tripal_cv_obo_add_db($dbname);
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if(!$db){
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- print "Cannot find database '$dbname' in Chado.\n";
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- return 0;
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+ tripal_cv_obo_quiterror("Cannot find database '$dbname' in Chado.");
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}
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- // check to see if the cvterm already exists
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- $cvtermsql = "SELECT * from {cvterm} WHERE name = '%s' and cv_id = %d";
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- $cvterm = db_fetch_object(db_query($cvtermsql,$name,$cv->cv_id));
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// if the cvterm doesn't exist then add it otherwise just update it
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+ $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname));
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if(!$cvterm){
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// check to see if the dbxref exists if not, add it
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$dbxref = tripal_cv_obo_add_dbxref($db->db_id,$accession);
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if(!$dbxref){
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- print "Failed to find or insert the dbxref record for cvterm, $name (id: $accession), for database $dbname\n";
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- return 0;
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+ tripal_cv_obo_quiterror("Failed to find or insert the dbxref record for cvterm, $name (id: $accession), for database $dbname");
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}
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// now add the cvterm
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@@ -416,11 +597,18 @@ function tripal_cv_obo_add_cv_term($term,$cv,$is_relationship = 0,$update = 1){
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";
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if(!db_query($sql,$cv->cv_id,$name,$definition,
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$dbxref->dbxref_id,$is_obsolete,$is_relationship)){
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- print "Failed to insert the term: $id\n";
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- return 0;
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+ if(!$is_relationship){
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+ tripal_cv_obo_quiterror("Failed to insert the term: $name ($dbname)");
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+ } else {
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+ tripal_cv_obo_quiterror("Failed to insert the relationship term: $name (cv: " . $cvname . " db: $dbname)");
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+ }
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}
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- print "Added CV term: $id\n";
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- $cvterm = db_fetch_object(db_query($cvtermsql,$name,$cv->cv_id));
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+ $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname));
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+ if(!$is_relationship){
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+ print "Added CV term: $name ($dbname)\n";
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+ } else {
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+ print "Added relationship CV term: $name ($dbname)\n";
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|
+ }
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}
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|
elseif($update) { // update the cvterm
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$sql = "
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@@ -430,11 +618,14 @@ function tripal_cv_obo_add_cv_term($term,$cv,$is_relationship = 0,$update = 1){
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|
";
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if(!db_query($sql,$term['name'][0],$definition,
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|
|
$is_obsolete,$is_relationship,$cvterm->cvterm_id)){
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|
- print "Failed to update the term: $name\n";
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|
- return 0;
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|
+ tripal_cv_obo_quiterror("Failed to update the term: $name");
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|
|
}
|
|
|
- print "Updated CV term: $id\n";
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|
|
- $cvterm = db_fetch_object(db_query($cvtermsql,$name,$cv->cv_id));
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|
|
+ $cvterm = db_fetch_object(db_query($cvtermsql,$name,$dbname));
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|
|
+ if(!$is_relationship){
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|
|
+ print "Updated CV term: $name ($dbname)\n";
|
|
|
+ } else {
|
|
|
+ print "Updated relationship CV term: $name ($dbname)\n";
|
|
|
+ }
|
|
|
}
|
|
|
// return the cvterm
|
|
|
return $cvterm;
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|
|
@@ -444,8 +635,14 @@ function tripal_cv_obo_add_cv_term($term,$cv,$is_relationship = 0,$update = 1){
|
|
|
*/
|
|
|
function tripal_cv_obo_add_cvterm_dbxref($cvterm,$xref){
|
|
|
|
|
|
- $accession = preg_replace('/^.+?:(.*)$/','\1',$xref);
|
|
|
- $dbname = preg_replace('/^(.+?):.*$/','\1',$xref);
|
|
|
+ $dbname = preg_replace('/^(.+?):.*$/','$1',$xref);
|
|
|
+ $accession = preg_replace('/^.+?:\s*(.*?)(\{.+$|\[.+$|\s.+$|\".+$|$)/','$1',$xref);
|
|
|
+ $description = preg_replace('/^.+?\"(.+?)\".*?$/','$1',$xref);
|
|
|
+ $dbxrefs = preg_replace('/^.+?\[(.+?)\].*?$/','$1',$xref);
|
|
|
+
|
|
|
+ if(!$accession){
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|
|
+ tripal_cv_obo_quiterror("Cannot add a dbxref without an accession: '$xref'");
|
|
|
+ }
|
|
|
|
|
|
// if the xref is a database link, handle that specially
|
|
|
if(strcmp($dbname,'http')==0){
|
|
|
@@ -456,13 +653,14 @@ function tripal_cv_obo_add_cvterm_dbxref($cvterm,$xref){
|
|
|
// check to see if the database exists
|
|
|
$db = tripal_cv_obo_add_db($dbname);
|
|
|
if(!$db){
|
|
|
- print "Cannot find database '$dbname' in Chado.";
|
|
|
- return 0;
|
|
|
+ tripal_cv_obo_quiterror("Cannot find database '$dbname' in Chado.");
|
|
|
}
|
|
|
|
|
|
// now add the dbxref
|
|
|
- $dbxref = tripal_cv_obo_add_dbxref($db->db_id,$accession);
|
|
|
- if(!$dbxref){ return 0;}
|
|
|
+ $dbxref = tripal_cv_obo_add_dbxref($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
|
|
|
$sql = "SELECT * from {cvterm_dbxref} WHERE cvterm_id = %d and dbxref_id = %d";
|
|
|
@@ -470,8 +668,7 @@ function tripal_cv_obo_add_cvterm_dbxref($cvterm,$xref){
|
|
|
$sql = "INSERT INTO {cvterm_dbxref} (cvterm_id,dbxref_id)".
|
|
|
"VALUES (%d,%d)";
|
|
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if(!db_query($sql,$cvterm->cvterm_id,$dbxref->dbxref_id)){
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- print "Cannot add cvterm_dbxref: $accession\n";
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- return 0;
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+ tripal_cv_obo_quiterror("Cannot add cvterm_dbxref: $xref");
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}
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}
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return 1;
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@@ -490,9 +687,9 @@ function tripal_cv_obo_add_dbxref($db_id,$accession,$version='',$description='')
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VALUES (%d,'%s','%s','%s')
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";
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if(!db_query($sql,$db_id,$accession,$version,$description)){
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- print "Failed to insert the dbxref record $accession\n";
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- return 0;
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+ tripal_cv_obo_quiterror("Failed to insert the dbxref record $accession");
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}
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+ print "Added Dbxref accession: $accession\n";
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$dbxref = db_fetch_object(db_query($dbxsql,$db_id,$accession));
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}
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return $dbxref;
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@@ -570,11 +767,4 @@ function tripal_cv_obo_parse($obo_file,&$obo,&$header){
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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_obo_loader_done (){
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- // return the search path to normal
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- db_query("set search_path to public");
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- return '';
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-}
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+
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spficklin