Committing to switch branches

tripal_cv/includes/obo_loader.inc

@@ -222,7 +222,7 @@ function tripal_cv_load_obo_v1_2_file($obo_name, $file, $jobid = NULL, $is_new =
   if ($is_new) {
     tripal_cv_load_obo_add_ref($obo_name, $file);
   }
-  print "Ontology Sucessfully loaded!\n";
+  print "\nOntology Sucessfully loaded!\n";
 
   // update the cvtermpath table
   tripal_cv_load_update_cvtermpath($newcvs, $jobid);
@@ -348,19 +348,12 @@ function tripal_cv_load_obo_v1_2($file, $jobid = NULL, &$newcvs) {
   $newcvs[$header['default-namespace'][0]] = $defaultcv->cv_id;
 
   // add any typedefs to the vocabulary first
-  $sql = "
-    SELECT * FROM tripal_obo_temp
-    WHERE type = 'Typedef' 
-  ";
-  $typedefs = chado_query($sql);
-  while ($typedef = db_fetch_object($typedefs)) {
-    $term = unserialize(base64_decode($typedef->stanza));
-    tripal_cv_obo_process_term($term, $defaultcv->name, 1, $newcvs, $default_db);
-  }
+  print "\nStep 2: Loading type defs...\n"; 
+  tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid);
 
   // next add terms to the vocabulary
-  print "\nStep 2: Loading terms...\n";  
-  if (!tripal_cv_obo_process_terms($defaultcv->name, $jobid, $newcvs, $default_db)) {
+  print "\nStep 3: Loading terms...\n";  
+  if (!tripal_cv_obo_process_terms($defaultcv, $jobid, $newcvs, $default_db)) {
     tripal_cv_obo_quiterror('Cannot add terms from this ontology');
   }
 
@@ -380,6 +373,58 @@ function tripal_cv_obo_quiterror($message) {
 
 }
 
+/*
+ * 
+ */
+function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid){
+  $sql = "
+    SELECT * 
+    FROM tripal_obo_temp
+    WHERE type = 'Typedef' 
+  ";
+  $typedefs = chado_query($sql);
+  
+    $sql = "
+    SELECT count(*) as num_terms
+    FROM tripal_obo_temp
+    WHERE type = 'Typedef'     
+  "; 
+  $result = db_fetch_object(chado_query($sql));
+  $count = $result->num_terms;
+  
+  // calculate the interval for updates
+  $interval = intval($count * 0.0001);
+  if ($interval < 1) {
+    $interval = 1;
+  }
+  $i = 0;
+  while ($typedef = db_fetch_object($typedefs)) {
+    $term = unserialize(base64_decode($typedef->stanza));
+    
+    // update the job status every interval
+    if ($jobid and $i % $interval == 0) {
+      $complete = ($i / $count) * 33.33333333;
+      tripal_job_set_progress($jobid, intval($complete + 33.33333333)); 
+      printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));                                                             
+    } 
+    
+    tripal_cv_obo_process_term($term, $defaultcv->name, 1, $newcvs, $default_db);
+    
+    $i++;
+  }
+    // set the final status
+  if ($jobid) {
+    if ($count > 0) {
+      $complete = ($i / $count) * 33.33333333;
+    }
+    else {
+      $complete = 33.33333333;
+    }
+    tripal_job_set_progress($jobid, intval($complete + 33.33333333)); 
+    printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
+  }  
+  return 1;
+}
 /**
  *
  * @ingroup tripal_obo_loader
@@ -391,11 +436,18 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
   // iterate through each term from the OBO file and add it
   $sql = "
     SELECT * FROM tripal_obo_temp
-    WHERE type = 'Term' 
+    WHERE type = 'Term'
     ORDER BY id
   ";
   $terms = chado_query($sql);
-  $count = pg_num_rows($terms);
+  
+  $sql = "
+    SELECT count(*) as num_terms
+    FROM tripal_obo_temp
+    WHERE type = 'Term'     
+  "; 
+  $result = db_fetch_object(chado_query($sql));
+  $count = $result->num_terms;
   
   // calculate the interval for updates
   $interval = intval($count * 0.0001);
@@ -407,13 +459,13 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
     
     // update the job status every interval
     if ($jobid and $i % $interval == 0) {
-      $complete = ($i / $count) * 50;
-      tripal_job_set_progress($jobid + 50, intval($complete)); 
-      printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 2, number_format(memory_get_usage()));                                                             
+      $complete = ($i / $count) * 33.33333333;
+      tripal_job_set_progress($jobid, intval($complete + 66.666666)); 
+      printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));                                                             
     }                                 
     
     // add/update this term
-    if (!tripal_cv_obo_process_term($term, $defaultcv, 0, $newcvs, $default_db)) {
+    if (!tripal_cv_obo_process_term($term, $defaultcv->name, 0, $newcvs, $default_db)) {
       tripal_cv_obo_quiterror("Failed to process terms from the ontology");
     }
 
@@ -422,9 +474,14 @@ function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $defau
   
   // set the final status
   if ($jobid) {
-    $complete = ($i / $count) * 50;
-    tripal_job_set_progress($jobid + 50, intval($complete)); 
-    printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 2, number_format(memory_get_usage()));
+    if ($count > 0) {
+      $complete = ($i / $count) * 33.33333333;
+    }
+    else {
+      $complete = 33.33333333;
+    }
+    tripal_job_set_progress($jobid, intval($complete + 66.666666)); 
+    printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
   }                                                             
   
   return 1;
@@ -810,7 +867,7 @@ function tripal_cv_obo_parse($obo_file, &$header, $jobid) {
     if ($jobid and $intv_read >= $interval) {            
       $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
       print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
-      tripal_job_set_progress($jobid, intval(($num_read / $filesize) * 50));
+      tripal_job_set_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
       $intv_read = 0;      
     }
     
@@ -895,6 +952,9 @@ function tripal_cv_obo_parse($obo_file, &$header, $jobid) {
       watchdog('T_obo_loader', "ERROR: Cannot insert stanza into temporary table.", array(), 'error');
       exit;
     }
+    $percent = sprintf("%.2f", ($num_read / $filesize) * 100);
+    print "Parsing Line $line_num (" . $percent . "%). Memory: " . number_format(memory_get_usage()) . " bytes.\r";
+    tripal_job_set_progress($jobid, intval(($num_read / $filesize) * 33.33333333));
   }
   return $default_db;
 }

tripal_pub/includes/pubmed.inc

@@ -74,10 +74,12 @@ function tripal_pub_remote_search_pubmed_range($terms, $start = 0, $limit = 10)
     $query = tripal_pub_remote_search_pubmed_query($terms); 
     
     // second retrieve the individual record
-    $pub_xml = tripal_pub_remote_search_pubmed_fetch($terms, $query['QueryKey'], $query['WebEnv'], 'xml', 0, 1); 
-    $pubs[] = $pub_xml;
+    $pub_xml = tripal_pub_remote_search_pubmed_fetch($terms, $query['QueryKey'], $query['WebEnv'], 'xml', 0, 1);
+    $pub = tripal_pub_remote_search_pubmed_parse_pubxml($pub_xml);
+    $pubs[] = $pub;    
     
   } 
+  dpm($pubs);
   return $pubs;
 }
 
@@ -161,11 +163,11 @@ function tripal_pub_remote_search_pubmed_parse_pubxml($pub_xml) {
   while ($xml->read()) {    
     $element = $xml->name;    
     if ($xml->nodeType == XMLReader::ELEMENT) {
-      $xml->read();
-      $value = $xml->value;
+      
       switch ($element) {
         case 'PMID':
-          $pub['pub_accession'] = $value;
+          $xml->read(); // get the value for this element
+          $pub['pub_accession'] = $xml->value;
           $pub['pub_database'] = 'PMID';
           break;        
         case 'Article':
@@ -184,22 +186,25 @@ function tripal_pub_remote_search_pubmed_parse_pubxml($pub_xml) {
 function tripal_pub_remote_search_pubmed_parse_article($xml, &$pub) {
     
   while ($xml->read()) {
-    $element = $xml->name;  
+    // get this element name
+    $element = $xml->name;     
+        
     // if we're at the </Article> element then we're done with the article...
-    if ($xml->nodeType == XMLReader::END_ELEMENT and $element = 'Article') {
+    if ($xml->nodeType == XMLReader::END_ELEMENT and $element == 'Article') {
       return;  
     }
-    if ($xml->nodeType == XMLReader::ELEMENT) {
-      $element = $xml->name;
-      $xml->read();
-      $value = $xml->value;
+    if ($xml->nodeType == XMLReader::ELEMENT) {    
       switch ($element) {
         case 'Journal':
           tripal_pub_remote_search_pubmed_parse_journal($xml, $pub);
           break;
         case 'ArticleTitle':
+          $xml->read();
+          $pub['title'] = $xml->value;
           break;
         case 'AbstractText':
+          $xml->read();
+          $pub['abstract'] = $xml->value;
           break;
         case 'Affiliation':
           break;
@@ -207,6 +212,8 @@ function tripal_pub_remote_search_pubmed_parse_article($xml, &$pub) {
           tripal_pub_remote_search_pubmed_parse_authorlist($xml, $pub);
           break;
         case 'Language':
+          $xml->read();
+          $pub['language'] = $xml->value;
           break;
         case 'ArticleDate':
           break; 
@@ -226,7 +233,7 @@ function tripal_pub_remote_search_pubmed_parse_journal($xml, &$pub) {
       
     if ($xml->nodeType == XMLReader::END_ELEMENT){
       // if we're at the </AuthorList> element then we're done with the article...
-      if($element = 'Journal') {
+      if($element == 'Journal') {
         return;
       }
     }
@@ -273,8 +280,6 @@ function tripal_pub_remote_search_pubmed_parse_authorlist($xml, &$pub) {
       }  
     }
     if ($xml->nodeType == XMLReader::ELEMENT) {
-      $xml->read();
-      $value = $xml->value;
       switch ($element) {
         case 'Author':          
           break;

tripal_pub/includes/remote_search.inc

@@ -23,8 +23,7 @@ function tripal_pub_remote_search_page() {
   $pager = theme('pager');
   
   // join all to form the final page
-  $output = $form . "<p><b>Found " . number_format($total_items) . " Results</b></br>" . $table . '</p>' . $pager;
-    dpm($results);
+  $output = $form . "<p><b>Found " . number_format($total_items) . " Results</b></br>" . $table . '</p>' . $pager;    
   
   return $output;
 }