Movoed obo_loader.php to tripal_cv

tripal_core/obo_loader.php

@@ -1,560 +0,0 @@
-<?php
-/*************************************************************************
-*
-*/
-function tripal_core_load_obo_job (){
-   global $user;
-
-#   $file = 'ro.obo'; 
-   $file = 'so_2_4_4.obo';
-   $args = array($file);
-   tripal_add_job("Load OBO $file",'tripal_core',
-      "tripal_core_load_obo_v1_2",$args,$user->uid);
-
-   return '';
-}
-/*************************************************************************
-*
-*/
-function tripal_core_load_obo_v1_2($file) {
-
-   $header = array();
-   $obo = array();
-   
-   $obo_file = drupal_get_path('module', 'tripal_core')."/$file";
-   print "Opening File $obo_file\n";
-
-   // set the search path
-   db_query("set search_path to chado,public");  // TODO: fix this
-
-   // make sure we have an 'internal' and a '_global' database
-   if(!tripal_core_obo_add_db('internal')){
-      return tripal_core_obo_loader_done();
-   }
-   if(!tripal_core_obo_add_db('_global')){
-      return tripal_core_obo_loader_done();
-   }
-
-   // parse the obo file
-   tripal_core_obo_parse($obo_file,$obo,$header);
-
-   // add the CV for this ontology to the database
-   $cv = tripal_core_obo_add_cv($header['default-namespace'][0],'');
-   if(!$cv){
-      return tripal_core_obo_loader_done();
-   }  
-
-   // add any typedefs to the vocabulary first
-   $typedefs = $obo['Typedef'];
-   foreach($typedefs as $typedef){
-      tripal_core_obo_add_cv_term($typedef,$cv,1);  
-   }
-
-   // next add terms to the vocabulary
-   $terms = $obo['Term'];
-   if(!tripal_core_obo_process_terms($terms,$cv,$obo)){
-      return tripal_core_obo_loader_done();   
-   }
-   return tripal_core_obo_loader_done();
-}
-
-/*************************************************************************
-*
-*/
-function tripal_core_obo_process_terms($terms,$cv,$obo){
-
-   foreach ($terms as $term){
-
-      // add the cvterm
-      $cvterm = tripal_core_obo_add_cv_term($term,$cv);
-      if(!$cvterm){ return 0; }
-      if(isset($term['is_anonymous'])){
-      }
-      if(isset($term['alt_id'])){
-      }
-      if(isset($term['subset'])){
-      }
-      // add synonyms for this cvterm
-      if(isset($term['synonym'])){
-         if(!tripal_core_obo_add_synonyms($term,$cvterm)){
-            return 0;
-         }
-      }
-      if(isset($term['exact_synonym'])){
-      }
-      if(isset($term['narrow_synonym'])){
-      }
-      if(isset($term['broad_synonym'])){
-      }
-      if(isset($term['xref'])){
-      }
-      if(isset($term['xref_analog'])){
-      }
-      if(isset($term['xref_unk'])){
-      }
-      // add is_a relationships for this cvterm
-      if(isset($term['is_a'])){
-         foreach($term['is_a'] as $is_a){
-            if(!tripal_core_obo_add_relationship($cvterm,$cv,$obo,'is_a',$is_a)){
-               return 0;
-            }
-         }
-      } 
-      if(isset($term['intersection_of'])){
-      }
-      if(isset($term['union_of'])){
-      }
-      if(isset($term['disjoint_from'])){
-      }
-      if(isset($term['relationship'])){
-         foreach($term['relationship'] as $value){
-            $rel = preg_replace('/^(.+?)\s.+?$/','\1',$value);
-            $object = preg_replace('/^.+?\s(.+?)$/','\1',$value);
-            if(!tripal_core_obo_add_relationship($cvterm,$cv,$obo,$rel,$object)){
-               return 0;
-            }
-         }
-      }
-      if(isset($term['replaced_by'])){
-      }
-      if(isset($term['consider'])){
-      }
-      if(isset($term['use_term'])){
-      }
-      if(isset($term['builtin'])){
-      }
-   }   
-   return 1;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_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')",$dbname)){
-         print "Cannot create '$dbname' db in Chado.";
-         return 0;
-      }      
-     $db = db_fetch_object(db_query($db_sql,$dbname));
-   }
-   return $db;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_add_cv($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)){
-         print "Failed to create the CV record";
-         return 0;
-      }
-      $cv = db_fetch_object(db_query($cv_sql,$vocab));
-   } else {
-      $sql = "UPDATE {cv} SET definition = '%s' WHERE name ='%s'";
-      if(!db_query($sql,$remark,$vocab)){
-         print "Failed to update the CV record";
-         return 0;
-      }
-      $cv = db_fetch_object(db_query($cv_sql,$vocab));
-   }
-   return $cv;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_add_cvterm_prop($cvterm,$property,$value,$rank){
-
-   // make sure the 'cvterm_property_type' CV exists
-   $cv = tripal_core_obo_add_cv($property,'');
-   if(!$cv){ return 0; }
-
-   // 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),
-      );
-      $cvproptype = tripal_core_obo_add_cv_term($term,$cv,0,0);
-      if(!$cvproptype){  return 0; }      
-   }
-
-
-   // 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)){
-      print "Could not add property $property for term\n";
-      return 0;
-   }
-   return 1;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_add_relationship($cvterm,$cv,$obo,$rel,$objname){
-
-   // make sure the relationship cvterm exists
-   $sql = "
-        SELECT * 
-        FROM {cvterm} CVT INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
-        WHERE CVT.name = '%s' and CV.name = '%s'
-   ";
-   if(strcmp($rel,'is_a')==0){ // is_a is part of the OBO format and is in the 'relationship' ontology
-      $cvisa = db_fetch_object(db_query($sql,$rel,'relationship'));
-   } else {
-      $cvisa = db_fetch_object(db_query($sql,$rel,$cv->name));
-   }
-   if(!$cvisa){
-      print "Cannot find the relationship term: $rel\n";
-      return 0;
-   }
-
-   // get the object term
-   $objterm = tripal_core_obo_get_term($obo,$objname);
-   if(!$objterm) { 
-      print "Could not find object term $objname\n";
-      return 0; 
-   }
-   $objcvterm = tripal_core_obo_add_cv_term($objterm,$cv);
-   if(!$objcvterm){ return 0; }
-
-   // 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,$cvisa->cvterm_id,$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,$cvisa->cvterm_id,$cvterm->cvterm_id,$objcvterm->cvterm_id)){
-         print "Cannot add $rel relationship";
-         return 0;
-      }
-//      print  "  $rel $objname\n";
-   }
-
-   return 1;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_get_term($obo,$id){
-   foreach ($obo as $type){
-      foreach ($type as $term){
-         $accession = $term['id'][0];
-         if(strcmp($accession,$id)==0){
-            return $term;
-         }
-      }
-   }
-   return;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_add_synonyms($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)){
-
-         print "Failed to add the synonyms type vocabulary";
-         return 0;
-      }
-   }
-
-   // 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:$type"),
-               'definition' => array(''),
-               'is_obsolete' => array(0),
-            );
-            if(!tripal_core_obo_add_cv_term($term,$syncv)){
-               return 0;
-            }
-            $syntype = db_fetch_object(db_query($cvtsql,$type,'synonym_type'));
-         }       
-
-         // make sure the synonym doesn't already exists
-         $sql = "
-            SELECT * 
-            FROM {cvtermsynonym} 
-            WHERE cvterm_id = %d and synonym = '%s' and type_id = %d
-         ";
-         $syn = db_fetch_object(db_query($sql,$cvterm->cvterm_id,$def,$syntype->cvterm_id));
-         if(!$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)){
-               print "Failed to insert the synonym for term: $name ($def)\n";
-               return 0;
-            }
-         }            
-      } 
-   }
-   return 1;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_add_cv_term($term,$cv,$is_relationship = 0,$update = 1){
-
-   // get the term properties
-   $name = $term['name'][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;
-   }
-
-   // get the accession and the database from the cvterm
-   $accession = preg_replace('/^.+?:(.*)$/','\1',$term['id'][0]);
-   $db = preg_replace('/^(.+?):.*$/','\1',$term['id'][0]);
-
-   // check to see if the database exists
-   $db = tripal_core_obo_add_db($db);
-   if(!$db){
-      print "Cannot find database '$db' in Chado.";
-      return 0;
-   }
-
-   // check to see if the cvterm already exists
-   $cvtermsql = "SELECT * from {cvterm} WHERE name = '%s' and cv_id = %d";
-   $cvterm = db_fetch_object(db_query($cvtermsql,$name,$cv->cv_id));
-
-   // if the cvterm doesn't exist then add it otherwise just update it
-   if(!$cvterm){
-      // check to see if the dbxref exists if not, add it
-      $dbxsql =  tripal_core_obo_add_dbxref($db->db_id,$accession);
-      if(!$dbxref){
-         print "Failed to find or insert the dbxref record for cvterm: $name ($accession)";
-         return 0;
-      }
-
-      // 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)){
-         print "Failed to insert the term: " . $term['name'][0];
-         return 0;
-      }     
-      print "Added CV term: $name\n";
-      $cvterm = db_fetch_object(db_query($cvtermsql,$name,$cv->cv_id));
-   }
-   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)){
-         print "Failed to update the term: $name\n";
-         return 0;
-      }  
-      print "Updated CV term: $name\n";
-      $cvterm = db_fetch_object(db_query($cvtermsql,$name,$cv->cv_id));         
-   }
-
-   // add the comment to the cvtermprop table
-   if(isset($term['comment'])){
-      $comments = $term['comment'];
-      $j = 0;
-      foreach($comments as $comment){
-         if(!tripal_core_obo_add_cvterm_prop($cvterm,'comment',$comment,$j)){
-            return 0;
-         }
-         $j++;
-      }
-   }
- 
-
-   // add any other external dbxrefs
-   if(isset($term['xref'])){
-      foreach($term['xref'] as $xref){
-         $accession = preg_replace('/^.+?:(.*)$/','\1',$xref);
-         $dbname = preg_replace('/^(.+?):.*$/','\1',$xref);
-
-         // if the xref is a database link, handle that specially
-         if(strcmp($db,'http')==0){
-            $accession = $xref;
-            $dbname = 'URL';
-         }
-
-         // check to see if the database exists
-         $db = tripal_core_obo_add_db($db);
-         if(!$db){
-            print "Cannot find database '$db' in Chado.";
-            return 0;
-         }
-
-         // now add the dbxref
-         $dbxref = tripal_core_obo_add_dbxref($db->db_id,$accession);
-         if(!$dbxref){ return 0;}
-
-         // 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)){
-               print "Cannot add cvterm_dbxref: $accession\n";
-               return 0;
-            }
-         }
-      }
-   }
-
-   // return the cvterm
-   return $cvterm;
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_add_dbxref($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)){
-         print "Failed to insert the dbxref record $accession\n";
-         return 0;
-      }
-      $dbxref = db_fetch_object(db_query($dbxsql,$db_id,$accession));
-   }
-   return $dbxref;
-
-}
-/*************************************************************************
-*
-*/
-function tripal_core_obo_parse($obo_file,&$obo,&$header){
-   $i = 0;
-   $in_header = 1;
-   $stanza = array();
-
-   $lines = file($obo_file,FILE_SKIP_EMPTY_LINES);
-
-   // iterate through the lines in the OBO file and parse the stanzas
-   foreach ($lines as $line_num => $line) {
-      $i++;
-
-      // remove newlines
-      $line = rtrim($line);  
-      // skip empty lines
-      if(strcmp($line,'')==0) { continue; }
-      //remove comments from end of lines
-      $line = preg_replace('/^(.*?)\!.*$/','\1',$line);  // TODO: if the explamation is escaped
-
-      if(preg_match('/^\s*\[/',$line)){  // at the first stanza we're out of header
-         $in_header = 0;
-         // load the stanza we just finished reading
-         if(sizeof($stanza) > 0){
-            if(!isset($obo[$type])){
-               $obo[$type] = array();
-            }
-            if(!isset($obo[$type][$stanza['id'][0]])){
-               $obo[$type][$stanza['id'][0]] = $stanza;
-            } else {
-               array_merge($obo[$type][$stanza['id'][0]],$stanza);
-            }
-         } 
-         // get the stanza type:  Term, Typedef or Instance
-         $type = preg_replace('/^\s*\[\s*(.+?)\s*\]\s*$/','\1',$line);
-
-         // start fresh with a new array
-         $stanza = array();
-         continue;
-      }
-      // break apart the line into the tag and value but ignore any escaped colons
-      preg_replace("/\\:/","|-|-|",$line); // temporarily replace escaped colons
-      $pair = explode(":",$line,2);
-      $tag = $pair[0];
-      $value = ltrim(rtrim($pair[1]));// remove surrounding spaces
-      $tag = preg_replace("/\|-\|-\|/","\:",$tag); // return the escaped colon
-      $value = preg_replace("/\|-\|-\|/","\:",$value);
-      if($in_header){
-         if(!isset($header[$tag])){
-            $header[$tag] = array();
-         }
-         $header[$tag][] = $value;
-      } else {
-         if(!isset($stanza[$tag])){
-            $stanza[$tag] = array();
-         }  
-         $stanza[$tag][] = $value;
-      }          
-   }
-   // now add the last term in the file
-   if(sizeof($stanza) > 0){
-      if(!isset($obo[$type])){
-         $obo[$type] = array();
-      }
-      if(!isset($obo[$type][$stanza['id'][0]])){
-         $obo[$type][$stanza['id'][0]] = $stanza;
-      } else {
-         array_merge($obo[$type][$stanza['id'][0]],$stanza);
-      }
-   }
-}
-
-/*************************************************************************
-*
-*/
-function tripal_core_obo_loader_done (){
-   // return the search path to normal
-   db_query("set search_path to public");  
-   return '';
-}